diff --git a/.github/workflows/deploy_jekyll.yml b/.github/workflows/deploy_jekyll.yml new file mode 100644 index 00000000..8e7f3434 --- /dev/null +++ b/.github/workflows/deploy_jekyll.yml @@ -0,0 +1,69 @@ +name: Deploy Jekyll site to Pages + +on: + # Runs on pushes targeting the default branch + push: + branches: [ "main" ] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +permissions: + contents: read + pages: write + id-token: write + +# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. +# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. +concurrency: + group: "pages" + cancel-in-progress: false + +jobs: + build: + runs-on: ubuntu-24.04 + defaults: + run: + working-directory: docs + steps: + - name: Checkout + uses: actions/checkout@v3 + - name: Setup Ruby + uses: ruby/setup-ruby@v1.204.0 + with: + ruby-version: '3.3' + bundler-cache: true + cache-version: 0 + - name: Setup Pages + id: pages + uses: actions/configure-pages@v3 + - name: Install dependencies + run: | + bundle install + - name: Build with Jekyll + # Outputs to the './_site' directory by default + run: | + bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" + env: + PAGES_REPO_NWO: ${{ github.repository }} + JEKYLL_ENV: production + JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + JEKYLL_BUILD_BRANCH: ${{ github.ref_name }} + JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }} + - name: Upload artifact + # Automatically uploads an artifact from the './_site' directory by default + uses: actions/upload-pages-artifact@v2 + + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + defaults: + run: + working-directory: docs + needs: build + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v2 diff --git a/.github/workflows/lint_jekyll.yaml b/.github/workflows/lint_jekyll.yaml new file mode 100644 index 00000000..fa8b0a3e --- /dev/null +++ b/.github/workflows/lint_jekyll.yaml @@ -0,0 +1,44 @@ +name: Lint Jekyll site + +on: [push, pull_request] + +jobs: + check-internal-links: + runs-on: ubuntu-latest + defaults: + run: + working-directory: docs + steps: + - uses: actions/checkout@v3 + - uses: ruby/setup-ruby@v1.196.0 + with: + ruby-version: '3.3' + bundler-cache: true + cache-version: 0 + - name: Setup Pages + id: pages + uses: actions/configure-pages@v3 + - name: Install dependencies + run: | + bundle install + - name: Build with Jekyll + # Outputs to the './_site' directory by default + run: | + bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" --strict_front_matter + env: + PAGES_REPO_NWO: ${{ github.repository }} + JEKYLL_ENV: production + JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + JEKYLL_BUILD_BRANCH: ${{ github.ref_name }} + JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }} + #- name: Validate HTML and check links + # run: | + # bundle exec htmlproofer \ + # --allow_missing_href=true \ + # --ignore-urls "/.*localhost.*/","/.*gitter\.im.*/" \ + # --enforce-https=false \ + # --disable-external=true \ + # --ignore_empty_alt=true \ + # --ignore_missing_alt=true \ + # --check-internal-hash=false \ + # ./_site \ No newline at end of file diff --git a/.gitignore b/.gitignore index d8fba58e..5a957bf4 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ .DS_Store __pycache__ results/test* -results/*/test* \ No newline at end of file +results/*/test* +docs/_site \ No newline at end of file diff --git a/docs/Gemfile b/docs/Gemfile new file mode 100644 index 00000000..1eabe643 --- /dev/null +++ b/docs/Gemfile @@ -0,0 +1,8 @@ +source "https://rubygems.org" + +# GitHub pages dependencies +gem 'github-pages', group: :jekyll_plugins + +# Webrick needed for Ruby v3.0+ compatibility +gem "webrick" +gem "html-proofer" \ No newline at end of file diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 00000000..9ccf3937 --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,49 @@ +title: Galaxy CoDex +# This appears in the html browser tab for the site title (seen mostly by search engines, not users) + +topnav_title: CoDex +# Optional: this appears on the top navigation bar next to the main_logo.svg icon + +description: "Galaxy Communities Dock (Galaxy Codex) is a catalog of Galaxy resources (i.e. tools, training, workflows) that can be filtered for any community." +# Metadata description of the website + +remote_theme: ELIXIR-Belgium/elixir-toolkit-theme + +theme_variables: + # biocommons blue + theme_color: 205a86 + datatables: + searchbuilder: True + topnav: + brand_logo: assets/img/galaxy_project_logo_square.png + +exclude: + - README.md + - CODE_OF_CONDUCT.md + - publications/* + - vendor + +defaults: + - + scope: + path: "pages" + type: "pages" + values: + permalink: /:basename + layout: "page" + sidebar: main + - + scope: + path: "index.md" + type: "pages" + values: + permalink: /:basename + layout: "page" + sidebar: main + +plugins: + - jemoji + - jekyll-sitemap + - jekyll-github-metadata + - webrick + - elixir-toolkit-theme-plugins diff --git a/docs/_data/CONTRIBUTORS.yml b/docs/_data/CONTRIBUTORS.yml new file mode 100644 index 00000000..5bcaa4d0 --- /dev/null +++ b/docs/_data/CONTRIBUTORS.yml @@ -0,0 +1,18 @@ + +############################ +### List of contributors ### +############################ + +### see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme + +############################################################################################################################################# +### add maintainers/contributors below and use their name in the contributors metadata section on each page they have contributed towards ### +############################################################################################################################################# + +# an example contributor is included below +# example roles include "lead", "first-author", "author", "editor", "workflow-tester" + +Johan Gustafsson: + git: supernord + orcid: 0000-0002-2977-5032 + affiliation: Australian BioCommons / University of Melbourne diff --git a/docs/_data/affiliations.yml b/docs/_data/affiliations.yml new file mode 100644 index 00000000..0e4bdda5 --- /dev/null +++ b/docs/_data/affiliations.yml @@ -0,0 +1,17 @@ +############################ +### List of affiliations ### +############################ + +### see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme + +######################################################################################################### +### add affiliations below and use the name(s) in the relevant metadata sections or code on each page ### +######################################################################################################### + +### add new affiliations below as needed + +#- name: Australian BioCommons +# image_url: /assets/img/biocommons_logo.png +# expose: true +# type: infrastructure +# url: https://www.biocommons.org.au/ diff --git a/docs/_data/footer.yml b/docs/_data/footer.yml new file mode 100644 index 00000000..22559773 --- /dev/null +++ b/docs/_data/footer.yml @@ -0,0 +1,6 @@ +# see https://github.com/AustralianBioCommons/human-omics-data-sharing-field-guide/blob/main/_data/footer.yml +#copyright: '' +#extra_line: Add other relevant information here! +#columns: +# - type: links +# width: 3 diff --git a/docs/_data/sidebars/main.yml b/docs/_data/sidebars/main.yml new file mode 100644 index 00000000..fe8d6228 --- /dev/null +++ b/docs/_data/sidebars/main.yml @@ -0,0 +1,8 @@ +subitems: + - title: About + url: /about + - title: Publications and online information + url: /project + - title: How-to contribute + url: /contributing + \ No newline at end of file diff --git a/docs/_data/tool_and_resource_list.yml b/docs/_data/tool_and_resource_list.yml new file mode 100644 index 00000000..7489a469 --- /dev/null +++ b/docs/_data/tool_and_resource_list.yml @@ -0,0 +1,36 @@ +- name: How to improve the annotation of Galaxy resources? + type: Hub post + description: Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources. + url: https://galaxyproject.org/news/2024-04-microgalaxy-hackathon/ +- name: GCC 2024 Training + type: Hub post + description: Collecting, Organizing, and Broadcasting Galaxy Tools for a Dedicated Scientific Community (using the Galaxy Tool Metadata Extractor Workflow). + url: https://galaxyproject.org/events/gcc2024/training/tool-finding/ +- name: Project 25 - ELIXIR BioHackathon in Barcelona + type: Hub post + description: Project 25 - Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities. + url: https://galaxyproject.org/news/2023-11-06-biohackathon/#project-25-increasing-the-findability-visibility-and-impact-of-galaxy-tools-for-specialised-scientific-communities +- name: Project 25 GitHub - BioHackathon Europe projects 2023 + type: Repository + description: Project 25 - Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities. + url: https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/25 +- name: microGalaxy SIG - microbial data analysis resources in Galaxy + type: Project using CoDex + description: Microbiology research involving microbiomes, meta*omics, and targeted microbial data analysis requires advanced programming skills, specialized tools, and significant computing power. Autonomous handling of these tasks can impede researchers’ progress. The microGalaxy Scientific Interest Group (SIG) is here to help! The microGalaxy SIG maintains the Galaxy Community Hub page and a dedicated microbial Galaxy subdomain - . + url: https://doi.org/10.7490/f1000research.1119768.1 +- name: ELIXIR Research Software Ecosystem (RSEc) + type: Project using CoDex + description: The ELIXIR Research Software Ecosystem (RSEc) is a project that centralizes and curates high-quality metadata for computational biology software tools, providing a unified resource for researchers. + url: https://research-software-ecosystem.github.io +- name: microGalaxy Technical Paper 2024 Preparation + type: Paper + description: This repository includes all the scripts written to produce figures in the paper along with the resulting figures. + url: https://github.com/usegalaxy-eu/microgalaxy_technical_paper_2024 +- name: Creation of an interactive Galaxy tools table for your community. + type: GTN tutorial + description: Create a community reviewed table for Galaxy tools within a specific scientific domain, and embed an interactive table in a community page. + url: https://gxy.io/GTN:T00426 +- name: Adding and updating best practice metadata for Galaxy tools using the bio.tools registry + type: GTN tutorial + description: Identify Galaxy tools without a bio.tools entry, create a bio.tools entry, update a bio.tools entry, add EDAM ontology terms to a bio.tools entry, and link a Galaxy tool to its corresponding bio.tools entry. + url: https://gxy.io/GTN:T00421 diff --git a/docs/_data/tools.yml b/docs/_data/tools.yml new file mode 100644 index 00000000..1316a1bb --- /dev/null +++ b/docs/_data/tools.yml @@ -0,0 +1,128204 @@ +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-limma + Conda version: 3.58.1 + Date of first commit of the suite: '2018-04-09' + Description: AskoR links EdgeR and AskOmics + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - askor_de + Galaxy wrapper id: askor + Galaxy wrapper owner: genouest + Galaxy wrapper parsed folder: https://github.com/genouest/galaxy-tools/tree/master/tools/askor + Galaxy wrapper source: https://github.com/genouest/galaxy-tools/tree/master/tools/askor + Galaxy wrapper version: '0.2' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/askomics/askoR + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Transcriptomics + ToolShed id: askor_de + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-03-03' + Description: A data source tool to fetch data from a BARIC Archive server. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - baric_archive_rennes + - baric_archive_toulouse + Galaxy wrapper id: baric_archive + Galaxy wrapper owner: genouest + Galaxy wrapper parsed folder: https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive + Galaxy wrapper source: https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://www.cesgo.org/catibaric/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Data Source + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-10-05' + Description: BRAKER is a pipeline for fully automated prediction of protein coding + gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - braker + Galaxy wrapper id: braker + Galaxy wrapper owner: genouest + Galaxy wrapper parsed folder: https://github.com/genouest/galaxy-tools/tree/master/tools/braker + Galaxy wrapper source: https://github.com/genouest/galaxy-tools/tree/master/tools/braker + Galaxy wrapper version: 2.1.6 + No. of tool users (5 years) (usegalaxy.eu): 165 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 165 + No. of tool users (all time) (usegalaxy.eu): 165 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 165 + Source: https://github.com/Gaius-Augustus/BRAKER + Status: To update + Tool usage (5 years) (usegalaxy.eu): 48 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 48 + Tool usage (all time) (usegalaxy.eu): 48 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 48 + ToolShed categories: + - Genome annotation + ToolShed id: braker + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-07-14' + Description: BRAKER3 is a pipeline for fully automated prediction of protein coding + gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . + EDAM operation: + - Genome annotation + - Gene prediction + EDAM operation (no superclasses): + - Genome annotation + - Gene prediction + EDAM topic: + - RNA-Seq + - Genomics + - Structure prediction + - Sequence analysis + EDAM topic (no superclasses): + - RNA-Seq + - Genomics + - Structure prediction + - Sequence analysis + Galaxy tool ids: + - braker3 + Galaxy wrapper id: braker3 + Galaxy wrapper owner: genouest + Galaxy wrapper parsed folder: https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 + Galaxy wrapper source: https://github.com/genouest/galaxy-tools/tree/master/tools/braker + Galaxy wrapper version: 3.0.8 + No. of tool users (5 years) (usegalaxy.eu): 1938 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 412 + No. of tool users (5 years) - all main servers: 2350 + No. of tool users (all time) (usegalaxy.eu): 1938 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 412 + No. of tool users (all time) - all main servers: 2350 + Source: https://github.com/Gaius-Augustus/BRAKER + Status: To update + Tool usage (5 years) (usegalaxy.eu): 294 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 71 + Tool usage (5 years) - all main servers: 365 + Tool usage (all time) (usegalaxy.eu): 294 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 71 + Tool usage (all time) - all main servers: 365 + ToolShed categories: + - Genome annotation + ToolShed id: braker3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: BRAKER3 is a pipeline for fully automated prediction of protein + coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes + bio.tool id: braker3 + bio.tool ids: + - braker3 + bio.tool name: BRAKER3 +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-bioperl + Conda version: 1.7.8 + Date of first commit of the suite: '2018-04-11' + Description: Convert FeelNC GTF to GFF3 + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - feelnc2asko + Galaxy wrapper id: feelnc2asko + Galaxy wrapper owner: genouest + Galaxy wrapper parsed folder: https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko + Galaxy wrapper source: https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/tderrien/FEELnc + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Convert Formats + ToolShed id: feelnc2asko + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: openjdk + Conda version: null + Date of first commit of the suite: '2021-09-16' + Description: Conversion from GCMS PostRun Analysis to Isocor + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - 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all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: openlabcds2csv + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-11-03' + Description: Proteogenomics workflow for the expert annotation of eukaryotic genomes + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - peptimapper_clustqualify + - peptimapper_clust_to_gff + - peptimapper_pep_match + - peptimapper_pep_novo_tag + Galaxy wrapper id: peptimapper + Galaxy wrapper owner: genouest + Galaxy wrapper parsed folder: https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper + Galaxy wrapper source: https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper + Galaxy wrapper version: '2.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Proteomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: requests + Conda version: null + Date of first commit of the suite: '2015-11-17' + Description: A suite of Galaxy tools designed to work with Ensembl REST API. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - get_feature_info + - get_genetree + - get_sequences + Galaxy wrapper id: Ensembl-REST + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 474 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 474 + No. of tool users (all time) (usegalaxy.eu): 2914 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2914 + Source: https://rest.ensembl.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 132 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 132 + Tool usage (all time) (usegalaxy.eu): 163 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 163 + ToolShed categories: + - Data Source + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.no: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2016-12-15' + Description: Gene Align and Family Aggregator + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gafa + Galaxy wrapper id: GAFA + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ + Galaxy wrapper version: 0.3.1 + No. of tool users (5 years) (usegalaxy.eu): 40 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 40 + No. of tool users (all time) (usegalaxy.eu): 47 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 47 + Source: http://aequatus.tgac.ac.uk + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Visualization + ToolShed id: gafa + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: treebest + Conda version: 1.9.2.post1 + Date of first commit of the suite: '2015-08-06' + Description: TreeBeST best + EDAM operation: + - Phylogenetic tree visualisation + - Phylogenetic analysis + - Phylogenetic inference (from molecular sequences) + EDAM operation (no superclasses): + - Phylogenetic tree visualisation + - Phylogenetic inference (from molecular sequences) + EDAM topic: + - Phylogenetics + EDAM topic (no superclasses): + - Phylogenetics + Galaxy tool ids: + - treebest_best + Galaxy wrapper id: TreeBest + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest + Galaxy wrapper version: 1.9.2.post0 + No. of tool users (5 years) (usegalaxy.eu): 1003 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1003 + No. of tool users (all time) (usegalaxy.eu): 1022 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1022 + Source: http://treesoft.sourceforge.net/treebest.shtml + Status: To update + Tool usage (5 years) (usegalaxy.eu): 48 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 48 + Tool usage (all time) (usegalaxy.eu): 52 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 52 + ToolShed categories: + - Phylogenetics + ToolShed id: treebest_best + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: TreeBeST, which stands for (gene) Tree Building guided by + Species Tree, is a versatile program that builds, manipulates and displays phylogenetic + trees. It is particularly designed for building gene trees with a known species + tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. + It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database + of Chris Ponting group. + bio.tool id: treebest + bio.tool ids: + - treebest + bio.tool name: TreeBeST +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: apoc + Conda version: 1b16 + Date of first commit of the suite: '2017-07-04' + Description: Large-scale structural comparison of protein pockets + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - apoc + Galaxy wrapper id: apoc + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ + Galaxy wrapper version: 1.0+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 4 + No. of tool users (5 years) (usegalaxy.org): 1 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5 + No. of tool users (all time) (usegalaxy.eu): 4 + No. of tool users (all time) (usegalaxy.org): 1 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5 + Source: http://cssb.biology.gatech.edu/APoc + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Computational chemistry + ToolShed id: apoc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-08-06' + Description: Convert 12- or 24-column BLAST output into 3-column hcluster_sg input + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - blast_parser + Galaxy wrapper id: blast_parser + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 417 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 417 + No. of tool users (all time) (usegalaxy.eu): 438 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 438 + Source: https://github.com/TGAC/earlham-galaxytools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 99 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 99 + Tool usage (all time) (usegalaxy.eu): 104 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 104 + ToolShed categories: + - Phylogenetics + ToolShed id: blast_parser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 7 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ete3 + Conda version: 3.1.1 + Date of first commit of the suite: '2018-10-11' + Description: Analyse phylogenetic trees using the ETE Toolkit + EDAM operation: + - Phylogenetic analysis + - Phylogenetic tree editing + EDAM operation (no superclasses): + - Phylogenetic tree editing + EDAM topic: + - Phylogenetics + EDAM topic (no superclasses): + - Phylogenetics + Galaxy tool ids: + - ete_gene_csv_finder + - ete_genetree_splitter + - ete_homology_classifier + - ete_init_taxdb + - ete_lineage_generator + - ete3_mod + - ete_species_tree_generator + Galaxy wrapper id: ete + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete + Galaxy wrapper version: 3.1.2 + No. of tool users (5 years) (usegalaxy.eu): 820 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 820 + No. of tool users (all time) (usegalaxy.eu): 966 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 966 + Source: http://etetoolkit.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 89 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 89 + Tool usage (all time) (usegalaxy.eu): 106 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 106 + ToolShed categories: + - Phylogenetics + ToolShed id: ete + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 7 + Tools available on UseGalaxy.no: 7 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + UseGalaxy.fr: 7 + UseGalaxy.no: 7 + biii: null + bio.tool description: The Environment for Tree Exploration (ETE) is a computational + framework that simplifies the reconstruction, analysis, and visualization of phylogenetic + trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous + improvements in the underlying library of methods, and providing a novel set of + standalone tools to perform common tasks in comparative genomics and phylogenetics. + The new features include (i) building gene-based and supermatrix-based phylogenies + using a single command, (ii) testing and visualizing evolutionary models, (iii) + calculating distances between trees of different size or including duplications, + and (iv) providing seamless integration with the NCBI taxonomy database. ETE is + freely available at http://etetoolkit.org + bio.tool id: ete + bio.tool ids: + - ete + bio.tool name: ete +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: EXPORT_DIR_PREFIX + Conda version: null + Date of first commit of the suite: '2016-01-18' + Description: Export datasets to cluster + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - export_to_cluster + Galaxy wrapper id: export_to_cluster + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ + Galaxy wrapper version: 0.0.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/TGAC/earlham-galaxytools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Data Export + ToolShed id: export_to_cluster + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: gblocks + Conda version: 0.91b + Date of first commit of the suite: '2018-04-11' + Description: Gblocks + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gblocks + Galaxy wrapper id: gblocks + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks + Galaxy wrapper version: 0.91b + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 466 + No. of tool users (5 years) - all main servers: 466 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 466 + No. of tool users (all time) - all main servers: 466 + Source: http://molevol.cmima.csic.es/castresana/Gblocks.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 62 + Tool usage (5 years) - all main servers: 62 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 62 + Tool usage (all time) - all main servers: 62 + ToolShed categories: + - Sequence Analysis + ToolShed id: gblocks + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2018-04-24' + Description: GeneSeqToFamily preparation converts data for the workflow + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gstf_preparation + Galaxy wrapper id: gstf_preparation + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation + Galaxy wrapper version: 0.4.3 + No. of tool users (5 years) (usegalaxy.eu): 377 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 377 + No. of tool users (all time) (usegalaxy.eu): 400 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 400 + Source: https://github.com/TGAC/earlham-galaxytools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 17 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 17 + ToolShed categories: + - Convert Formats + ToolShed id: gstf_preparation + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hcluster_sg + Conda version: 0.5.1 + Date of first commit of the suite: '2015-08-05' + Description: Hierarchically clustering on a sparse graph + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hcluster_sg + Galaxy wrapper id: hcluster_sg + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg + Galaxy wrapper version: 0.5.1.1 + No. of tool users (5 years) (usegalaxy.eu): 243 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 243 + No. of tool users (all time) (usegalaxy.eu): 263 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 263 + Source: https://github.com/douglasgscofield/hcluster + Status: To update + Tool usage (5 years) (usegalaxy.eu): 54 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 54 + Tool usage (all time) (usegalaxy.eu): 57 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 57 + ToolShed categories: + - Phylogenetics + ToolShed id: hcluster_sg + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-08-13' + Description: Converts hcluster_sg 3-column output into lists of ids + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hcluster_sg_parser + Galaxy wrapper id: hcluster_sg_parser + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser + Galaxy wrapper version: 0.2.1 + No. of tool users (5 years) (usegalaxy.eu): 266 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 266 + No. of tool users (all time) (usegalaxy.eu): 293 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 293 + Source: https://github.com/TGAC/earlham-galaxytools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 22 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 22 + Tool usage (all time) (usegalaxy.eu): 25 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 25 + ToolShed categories: + - Phylogenetics + ToolShed id: hcluster_sg_parser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: lotus2 + Conda version: 2.34.1 + Date of first commit of the suite: '2021-06-08' + Description: LotuS2 OTU processing pipeline + EDAM operation: + - Sequence feature detection + - DNA barcoding + EDAM operation (no superclasses): + - Sequence feature detection + - DNA barcoding + EDAM topic: + - Metagenomics + - Taxonomy + - Microbial ecology + EDAM topic (no superclasses): + - Metagenomics + - Taxonomy + - Microbial ecology + Galaxy tool ids: + - lotus2 + Galaxy wrapper id: lotus2 + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 + Galaxy wrapper version: '2.32' + No. of tool users (5 years) (usegalaxy.eu): 1219 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 37 + No. of tool users (5 years) - all main servers: 1256 + No. of tool users (all time) (usegalaxy.eu): 1219 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 37 + No. of tool users (all time) - all main servers: 1256 + Source: http://lotus2.earlham.ac.uk/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 182 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 186 + Tool usage (all time) (usegalaxy.eu): 182 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 186 + ToolShed categories: + - Metagenomics + ToolShed id: lotus2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: LotuS2 is a lightweight and user-friendly pipeline that is + fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering + steps to further increase data quality. High data usage rates and reliability + enable high-throughput microbiome analysis in minutes. + bio.tool id: lotus2 + bio.tool ids: + - lotus2 + bio.tool name: lotus2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: miranda + Conda version: 3.3a + Date of first commit of the suite: '2015-10-30' + Description: Finds potential target sites for miRNAs in genomic sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - miranda + Galaxy wrapper id: miranda + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda + Galaxy wrapper version: 3.3a+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 6408 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6408 + No. of tool users (all time) (usegalaxy.eu): 6514 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6514 + Source: http://www.microrna.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 94 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 94 + Tool usage (all time) (usegalaxy.eu): 99 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 99 + ToolShed categories: + - RNA + ToolShed id: miranda + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-preprocesscore + Conda version: 1.64.0 + Date of first commit of the suite: '2017-07-04' + Description: This tool can be used to plot heatmap of gene expression data. The + genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - plotheatmap + Galaxy wrapper id: plotheatmap + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Computational chemistry + ToolShed id: plotheatmap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rDock + Conda version: '2013.1' + Date of first commit of the suite: '2016-12-14' + Description: Docking ligands to proteins and nucleic acids + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rdock + Galaxy wrapper id: rdock + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://rdock.sourceforge.net/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Computational chemistry + ToolShed id: rdock + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2017-05-18' + Description: Replace chromosome names + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - replace_chromosome_names + Galaxy wrapper id: replace_chromosome_names + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 514 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 514 + No. of tool users (all time) (usegalaxy.eu): 573 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 573 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 69 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 69 + Tool usage (all time) (usegalaxy.eu): 83 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 83 + ToolShed categories: + - Text Manipulation + ToolShed id: replace_chromosome_names + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2016-01-29' + Description: Filter SNPs in RSAT Matrix Scan output + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rsat_filter_snps + Galaxy wrapper id: rsat_filter_snps + Galaxy wrapper owner: earlham + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/TGAC/earlham-galaxytools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - ChIP-seq + - Systems Biology + ToolShed id: rsat_filter_snps + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-bioperl + Conda version: 1.7.8 + Date of first commit of the suite: '2017-05-12' + Description: SMART domains + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - smart_domains + Galaxy wrapper id: smart_domains + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://smart.embl.de/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: smart_domains + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: smina + Conda version: 2017.11.9 + Date of first commit of the suite: '2017-07-07' + Description: smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses + on improving scoring and minimization + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - smina + Galaxy wrapper id: smina + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 499 + No. of tool users (5 years) (usegalaxy.org): 44 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 543 + No. of tool users (all time) (usegalaxy.eu): 499 + No. of tool users (all time) (usegalaxy.org): 44 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 543 + Source: https://sourceforge.net/projects/smina/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 10 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 26 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 10 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 26 + ToolShed categories: + - Computational chemistry + ToolShed id: smina + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: t-coffee + Conda version: 13.46.0.919e8c6b + Date of first commit of the suite: '2016-12-13' + Description: T-Coffee + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - t_coffee + Galaxy wrapper id: t_coffee + Galaxy wrapper owner: earlhaminst + Galaxy wrapper parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee + Galaxy wrapper source: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee + Galaxy wrapper version: 13.45.0.4846264 + No. of tool users (5 years) (usegalaxy.eu): 3783 + No. of tool users (5 years) (usegalaxy.org): 1 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3784 + No. of tool users (all time) (usegalaxy.eu): 9125 + No. of tool users (all time) (usegalaxy.org): 1 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 9126 + Source: http://www.tcoffee.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 211 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 212 + Tool usage (all time) (usegalaxy.eu): 229 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 230 + ToolShed categories: + - Sequence Analysis + ToolShed id: t_coffee + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mummer + Conda version: '3.23' + Date of first commit of the suite: '2019-11-20' + Description: Order and Orientate Contigs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - abacas + Galaxy wrapper id: abacas + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas + Galaxy wrapper source: https://github.com/phac-nml/abacas + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/abacas + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + ToolShed id: abacas + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-bioperl + Conda version: 1.7.8 + Date of first commit of the suite: '2017-10-13' + Description: Summarise an assembly (e.g. N50 metrics) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - assemblystats + Galaxy wrapper id: assemblystats + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats + Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/galaxy_tools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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bamclipper + Galaxy wrapper id: bamclipper + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper + Galaxy wrapper source: https://github.com/tommyau/bamclipper + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/tommyau/bamclipper + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: bamclipper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bio_hansel + Conda version: 2.6.1 + Date of first commit of the suite: '2018-08-01' + Description: Heidelberg and Enteritidis SNP Elucidation + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - biohansel + Galaxy wrapper id: biohansel + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel + Galaxy wrapper source: https://github.com/phac-nml/biohansel + Galaxy wrapper version: 2.4.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/biohansel + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: biohansel + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pandas + Conda version: null + Date of first commit of the suite: '2019-03-15' + Description: Convert BioHansel output data to a Bionumerics friendly form + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bionumeric_convert + Galaxy wrapper id: biohansel_bionumeric_converter + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter + Galaxy wrapper source: null + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/galaxy_tools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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bundle_collection + Galaxy wrapper id: bundle_collections + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections + Galaxy wrapper source: null + Galaxy wrapper version: 1.3.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 2 + No. of tool users (5 years) (usegalaxy.org.au): 1518 + No. of tool users (5 years) - all main servers: 1520 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 2 + No. of tool users (all time) (usegalaxy.org.au): 1526 + No. of tool users (all time) - all main servers: 1528 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 73 + Tool usage (5 years) - all main servers: 74 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 76 + Tool usage (all time) - all main servers: 77 + ToolShed categories: + - Sequence Analysis + ToolShed id: bundle_collections + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: gawk + Conda version: null + Date of first commit of the suite: '2015-12-10' + Description: Collection tool that collapses a list of files into a single datasset + in order of appears in collection + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - collapse_dataset + Galaxy wrapper id: collapse_collection + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection + Galaxy wrapper source: null + Galaxy wrapper version: 5.1.0 + No. of tool users (5 years) (usegalaxy.eu): 39518 + No. of tool users (5 years) (usegalaxy.org): 22007 + No. of tool users (5 years) (usegalaxy.org.au): 3969 + No. of tool users (5 years) - all main servers: 65494 + No. of tool users (all time) (usegalaxy.eu): 40471 + No. of tool users (all time) (usegalaxy.org): 24841 + No. of tool users (all time) (usegalaxy.org.au): 4101 + No. of tool users (all time) - all main servers: 69413 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3555 + Tool usage (5 years) (usegalaxy.org): 3536 + Tool usage (5 years) (usegalaxy.org.au): 814 + Tool usage (5 years) - all main servers: 7905 + Tool usage (all time) (usegalaxy.eu): 3629 + Tool usage (all time) (usegalaxy.org): 4045 + Tool usage (all time) (usegalaxy.org.au): 835 + Tool usage (all time) - all main servers: 8509 + ToolShed categories: + - Sequence Analysis + ToolShed id: collapse_collections + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2018-03-02' + Description: JSON collection tool that takes multiple JSON data arrays and combines + them into a single JSON array. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - combine_json + Galaxy wrapper id: combineJSON + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON + Galaxy wrapper source: null + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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csvtk_awklike_filter + - csvtk_awklike_mutate + - csvtk_collapse + - csvtk_concat + - csvtk_convert + - csvtk_correlation + - csvtk_cut + - csvtk_filter + - csvtk_freq + - csvtk_gather + - csvtk_join + - csvtk_mutate + - csvtk_plot + - csvtk_replace + - csvtk_sample + - csvtk_separate + - csvtk_sort + - csvtk_split + - csvtk_summary + - csvtk_uniq + Galaxy wrapper id: csvtk + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk + Galaxy wrapper source: https://github.com/shenwei356/csvtk + Galaxy wrapper version: 0.20.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://bioinf.shenwei.me/csvtk/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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fasta2bed + Galaxy wrapper id: fasta2bed + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed + Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/galaxy_tools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: fasta2bed + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-bioperl + Conda version: 1.7.8 + Date of first commit of the suite: '2016-10-26' + Description: extract single fasta from multiple fasta file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fa-extract-sequence + Galaxy wrapper id: fasta_extract + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract + Galaxy wrapper source: https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 10 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1286 + No. of tool users (5 years) - all main servers: 1296 + No. of tool users (all time) (usegalaxy.eu): 10 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1827 + No. of tool users (all time) - all main servers: 1837 + Source: https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 144 + Tool usage (5 years) - all main servers: 145 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 181 + Tool usage (all time) - all main servers: 182 + ToolShed categories: + - Sequence Analysis + ToolShed id: fasta_extract + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-bioperl + Conda version: 1.7.8 + Date of first commit of the suite: '2017-10-11' + Description: Summary multiple FastQC into a single tabular line report + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - FastQC_Summary + Galaxy wrapper id: fastqc_stats + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats + Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools + Galaxy wrapper version: '1.2' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/galaxy_tools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: fastqc_stats + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: feht + Conda version: 1.1.0 + Date of first commit of the suite: '2017-10-11' + Description: Automatically identify makers predictive of groups. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - feht + Galaxy wrapper id: feht + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht + Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/galaxy_tools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: feht + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-bioperl + Conda version: 1.7.8 + Date of first commit of the suite: '2017-10-12' + Description: Remove short and repeat contigs/scaffolds + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - filter_spades_repeat + Galaxy wrapper id: filter_spades_repeats + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats + Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools/ + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/galaxy_tools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + ToolShed id: filter_spades_repeats + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: srst2 + Conda version: 0.2.0 + Date of first commit of the suite: '2015-12-03' + Description: Download MLST datasets by species from pubmlst.org + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - getmlst + Galaxy wrapper id: getmlst + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst + Galaxy wrapper source: null + Galaxy wrapper version: 0.1.4.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: getmlst + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: gnali + Conda version: 1.1.0 + Date of first commit of the suite: '2020-03-30' + Description: A tool to find nonessential, loss-of-function gene variants + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gnali + Galaxy wrapper id: gnali + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali + Galaxy wrapper source: https://github.com/phac-nml/gnali/ + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/gnali/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: gnali + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hivtrace + Conda version: 1.5.0 + Date of first commit of the suite: '2015-12-10' + Description: An application that identifies potential transmission clusters within + a supplied FASTA file with an option to find potential links against the Los Alamos + HIV Sequence Database. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hivtrace + Galaxy wrapper id: hivtrace + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace + Galaxy wrapper source: https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: hivtrace + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: kaptive + Conda version: 3.0.0b5 + Date of first commit of the suite: '2017-04-10' + Description: Kaptive reports information about capsular (K) loci found in genome + assemblies. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - kaptive + Galaxy wrapper id: kaptive + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive + Galaxy wrapper source: null + Galaxy wrapper version: 0.3.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: kaptive + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: kat + Conda version: 2.4.2 + Date of first commit of the suite: '2017-03-13' + Description: Filtering kmers or reads from a database of kmers hashes + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - kat_@EXECUTABLE@ + Galaxy wrapper id: kat_filter + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter + Galaxy wrapper source: null + Galaxy wrapper version: '2.3' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: kat_filter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: kat + Conda version: 2.4.2 + Date of first commit of the suite: '2017-02-06' + Description: SEquence Coverage estimator Tool. Estimates the coverage of each sequence + in a file using K-mers from another sequence file. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - kat_@EXECUTABLE@ + Galaxy wrapper id: kat_sect + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect + Galaxy wrapper source: null + Galaxy wrapper version: '2.3' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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mauve_contig_mover + Galaxy wrapper id: mauve_contig_mover + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover + Galaxy wrapper source: https://github.com/phac-nml/mauve_contig_mover + Galaxy wrapper version: 1.0.10 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/mauve_contig_mover + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: mauve_contig_mover + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 2 + Conda id: mob_suite + Conda version: 3.1.9 + Date of first commit of the suite: '2018-08-20' + Description: MOB-suite is a set of software tools for clustering, reconstruction + and typing of plasmids from draft assemblies + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mob_recon + - mob_typer + Galaxy wrapper id: mob_suite + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite + Galaxy wrapper source: https://github.com/phac-nml/mob-suite + Galaxy wrapper version: 3.0.3 + No. of tool users (5 years) (usegalaxy.eu): 119024 + No. of tool users (5 years) (usegalaxy.org): 42 + No. of tool users (5 years) (usegalaxy.org.au): 36310 + No. of tool users (5 years) - all main servers: 155376 + No. of tool users (all time) (usegalaxy.eu): 119024 + No. of tool users (all time) (usegalaxy.org): 42 + No. of tool users (all time) (usegalaxy.org.au): 36310 + No. of tool users (all time) - all main servers: 155376 + Source: https://github.com/phac-nml/mob-suite + Status: To update + Tool usage (5 years) (usegalaxy.eu): 628 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 191 + Tool usage (5 years) - all main servers: 821 + Tool usage (all time) (usegalaxy.eu): 628 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 191 + Tool usage (all time) - all main servers: 821 + ToolShed categories: + - Sequence Analysis + ToolShed id: mob_suite + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mrbayes + Conda version: 3.2.7 + Date of first commit of the suite: '2015-12-04' + Description: A program for the Bayesian estimation of phylogeny. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mrbayes + Galaxy wrapper id: mrbayes + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes + Galaxy wrapper source: null + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: mrbayes + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2018-09-28' + Description: RScript to parse the results of mykrobe predictor. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mykrobe_parseR + Galaxy wrapper id: mykrobe_parser + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser + Galaxy wrapper source: https://github.com/phac-nml/mykrobe-parser + Galaxy wrapper version: 0.1.4.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/phac-nml/mykrobe-parser + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: mykrobe_parser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pangolin + Conda version: '4.3' + Date of first commit of the suite: '2020-05-01' + Description: Phylogenetic Assignment of Named Global Outbreak LINeages + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pangolin + Galaxy wrapper id: pangolin + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin + Galaxy wrapper source: https://github.com/hCoV-2019/pangolin + Galaxy wrapper version: 1.1.14 + No. of tool users (5 years) (usegalaxy.eu): 7457 + No. of tool users (5 years) (usegalaxy.org): 8518 + No. of tool users (5 years) (usegalaxy.org.au): 2760 + No. of tool users (5 years) - all main servers: 18735 + No. of tool users (all time) (usegalaxy.eu): 7457 + No. of tool users (all time) (usegalaxy.org): 8518 + No. of tool users (all time) (usegalaxy.org.au): 2760 + No. of tool users (all time) - all main servers: 18735 + Source: https://github.com/hCoV-2019/pangolin + Status: To update + Tool usage (5 years) (usegalaxy.eu): 508 + Tool usage (5 years) (usegalaxy.org): 377 + Tool usage (5 years) (usegalaxy.org.au): 259 + Tool usage (5 years) - all main servers: 1144 + Tool usage (all time) (usegalaxy.eu): 508 + Tool usage (all time) (usegalaxy.org): 377 + Tool usage (all time) (usegalaxy.org.au): 259 + Tool usage (all time) - all main servers: 1144 + ToolShed categories: + - Sequence Analysis + ToolShed id: pangolin + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-12-14' + Description: Extract Patristic Distance From a Tree + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - patrist + Galaxy wrapper id: patrist + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist + Galaxy wrapper source: https://github.com/phac-nml/patrist + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: influx_si_data_manager + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: influx_si + Conda version: 7.1.0 + Date of first commit of the suite: '2020-04-17' + Description: metabolic flux estimation based on [in]stationary labeling + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - influx_si + Galaxy wrapper id: influx_si + Galaxy wrapper owner: workflow4metabolomics + Galaxy wrapper parsed folder: https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si + Galaxy wrapper source: https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ + Galaxy wrapper version: 7.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/sgsokol/influx + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: influx_si + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-ipo + Conda version: 1.28.0 + Date of first commit of the suite: '2019-10-03' + Description: '[W4M][LC-MS] IPO' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - 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all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: ipo + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: isoplot + Conda version: 1.3.1 + Date of first commit of the suite: '2021-07-12' + Description: Isoplot is a software for the visualisation of MS data from C13 labelling + experiments + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - isoplot + Galaxy wrapper id: isoplot + Galaxy wrapper owner: workflow4metabolomics + Galaxy wrapper parsed folder: https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot + Galaxy wrapper source: https://github.com/llegregam/Isoplot/tree/main + Galaxy wrapper version: 1.3.0+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 4 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4 + No. of tool users (all time) (usegalaxy.eu): 4 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 3 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Metabolomics + - Visualization + ToolShed id: isoplot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2023-07-10' + Description: retrieves data from KMD HMDB API and produce plot and csv file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - kmd_hmdb_data_plot + Galaxy wrapper id: kmd_hmdb_data_plot + Galaxy wrapper owner: workflow4metabolomics + Galaxy wrapper parsed folder: https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot + Galaxy wrapper source: https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/workflow4metabolomics/tools-metabolomics + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: kmd_hmdb_data_plot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-lme4 + Conda version: null + Date of first commit of the suite: '2022-05-16' + Description: '[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance + for repeated measures using mixed model' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mixmodel4repeated_measures + Galaxy wrapper id: mixmodel4repeated_measures + Galaxy wrapper owner: workflow4metabolomics + Galaxy wrapper parsed folder: https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures + Galaxy wrapper source: https://github.com/workflow4metabolomics/tools-metabolomics + Galaxy wrapper version: 3.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://workflow4metabolomics.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: mixmodel4repeated_measures + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2022-03-15' + Description: '[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement + MSPurity.' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ms2snoop + Galaxy wrapper id: ms2snoop + Galaxy wrapper owner: workflow4metabolomics + Galaxy wrapper parsed folder: https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop + Galaxy wrapper source: null + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://workflow4metabolomics.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: ms2snoop + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-09-20' + Description: Convert mzML, mzXML or netCDF files to mzML or mzXML + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - 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all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: w4mconcatenate + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 12 + Available on UseGalaxy.fr: 12 + Available on UseGalaxy.org (Main): 9 + Available on UseGalaxy.org.au: 11 + Conda id: bioconductor-xcms + Conda version: 4.0.0 + Date of first commit of the suite: '2023-05-24' + Description: null + EDAM operation: + - Mass spectrum visualisation + - Label-free quantification + - Validation + - Filtering + - Chromatographic alignment + - Peak detection + - Chromatogram visualisation + EDAM operation (no superclasses): + - Mass spectrum visualisation + - Label-free quantification + - Validation + - Filtering + - Chromatographic alignment + - Peak detection + - Chromatogram visualisation + EDAM topic: + - Biological imaging + - Data visualisation + - Metabolomics + EDAM topic (no superclasses): + - Data visualisation + - Metabolomics + Galaxy tool ids: + - abims_xcms_fillPeaks + - abims_xcms_group + - abims_xcms_refine + - abims_xcms_retcor + - abims_xcms_summary + - abims_xcms_xcmsSet + - msnbase_readmsdata + - xcms_export_samplemetadata + - xcms_merge + - xcms_plot_chromatogram + - xcms_plot_eic + - xcms_plot_raw + Galaxy wrapper id: xcms + Galaxy wrapper owner: workflow4metabolomics + Galaxy wrapper parsed folder: https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms + Galaxy wrapper source: https://github.com/workflow4metabolomics/tools-metabolomics/ + Galaxy wrapper version: 4.0.0 + No. of tool users (5 years) (usegalaxy.eu): 31909 + No. of tool users (5 years) (usegalaxy.org): 7099 + No. of tool users (5 years) (usegalaxy.org.au): 5333 + No. of tool users (5 years) - all main servers: 44341 + No. of tool users (all time) (usegalaxy.eu): 35790 + No. of tool users (all time) (usegalaxy.org): 7099 + No. of tool users (all time) (usegalaxy.org.au): 5357 + No. of tool users (all time) - all main servers: 48246 + Source: https://github.com/sneumann/xcms + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1357 + Tool usage (5 years) (usegalaxy.org): 413 + Tool usage (5 years) (usegalaxy.org.au): 330 + Tool usage (5 years) - all main servers: 2100 + Tool usage (all time) (usegalaxy.eu): 1384 + Tool usage (all time) (usegalaxy.org): 413 + Tool usage (all time) (usegalaxy.org.au): 330 + Tool usage (all time) - all main servers: 2127 + ToolShed categories: + - Metabolomics + ToolShed id: xcms + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 6 + Tools available on UseGalaxy.cz: 10 + Tools available on UseGalaxy.eu: 12 + Tools available on UseGalaxy.fr: 12 + Tools available on UseGalaxy.no: 9 + Tools available on UseGalaxy.org (Main): 9 + Tools available on UseGalaxy.org.au: 11 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 6 + UseGalaxy.cz: 10 + UseGalaxy.eu: 12 + UseGalaxy.fr: 12 + UseGalaxy.no: 9 + UseGalaxy.or: 11 + biii: null + bio.tool description: Framework for processing and visualization of chromatographically + separated and single-spectra mass spectral data. The packages enables imports + from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, + untargeted analyte profiling. + bio.tool id: XCMS + bio.tool ids: + - XCMS + bio.tool name: xcms +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cfm + Conda version: '33' + Date of first commit of the suite: '2019-03-07' + Description: Competitive Fragmentation Modeling (CFM) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cfmid + Galaxy wrapper id: cfm + Galaxy wrapper owner: computational-metabolomics + Galaxy wrapper parsed folder: https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm + Galaxy wrapper source: https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm + Galaxy wrapper version: '33' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://sourceforge.net/p/cfm-id/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: cfmid + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: metfrag + Conda version: 2.4.5 + Date of first commit of the suite: '2020-06-30' + Description: '[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated + by MetFrag' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - metfrag_vis + Galaxy wrapper id: metfrag-vis + Galaxy wrapper owner: computational-metabolomics + Galaxy wrapper parsed folder: https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis + Galaxy wrapper source: https://github.com/computational-metabolomics/metfrag-galaxy + Galaxy wrapper version: 2.4.5+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 50 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 50 + No. of tool users (all time) (usegalaxy.eu): 50 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 50 + Source: https://github.com/computational-metabolomics/metfrag-galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 14 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 14 + Tool usage (all time) (usegalaxy.eu): 14 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 14 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: metfrag + Conda version: 2.4.5 + Date of first commit of the suite: '2019-08-01' + Description: '[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can + work with the output from msPurity)' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - metfrag + Galaxy wrapper id: metfrag + Galaxy wrapper owner: computational-metabolomics + Galaxy wrapper parsed folder: https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag + Galaxy wrapper source: https://github.com/computational-metabolomics/metfrag-galaxy + Galaxy wrapper version: 2.4.5+galaxy3 + No. of tool users (5 years) (usegalaxy.eu): 192 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 192 + No. of tool users (all time) (usegalaxy.eu): 192 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 192 + Source: https://github.com/computational-metabolomics/metfrag-galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 20 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 20 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 10 + Available on UseGalaxy.fr: 11 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-mspurity + Conda version: 1.28.0 + Date of first commit of the suite: '2019-05-24' + Description: '[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor + ion purity assessments, data processing and spectral matching for LC-MS(/MS) and + DI-MS(/MS) data' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mspurity_averagefragspectra + - mspurity_combineannotations + - mspurity_createdatabase + - mspurity_createmsp + - mspurity_dimspredictpuritysingle + - mspurity_filterfragspectra + - mspurity_flagremove + - mspurity_frag4feature + - mspurity_puritya + - mspurity_purityx + - mspurity_spectralmatching + Galaxy wrapper id: msPurity + Galaxy wrapper owner: computational-metabolomics + Galaxy wrapper parsed folder: https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity + Galaxy wrapper source: https://github.com/computational-metabolomics/mspurity-galaxy + Galaxy wrapper version: 1.28.0 + No. of tool users (5 years) (usegalaxy.eu): 848 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 848 + No. of tool users (all time) (usegalaxy.eu): 848 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 848 + Source: https://github.com/computational-metabolomics/mspurity-galaxy + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 91 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 91 + Tool usage (all time) (usegalaxy.eu): 91 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 91 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 10 + Tools available on UseGalaxy.eu: 10 + Tools available on UseGalaxy.fr: 11 + Tools available on UseGalaxy.no: 10 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 10 + UseGalaxy.eu: 10 + UseGalaxy.fr: 11 + UseGalaxy.no: 10 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2019-09-24' + Description: '[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor + ion purity assessments, data processing and spectral matching for LC-MS(/MS) and + DI-MS(/MS) data' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - msp_split + Galaxy wrapper id: msp_split + Galaxy wrapper owner: tomnl + Galaxy wrapper parsed folder: https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split + Galaxy wrapper source: https://github.com/computational-metabolomics/mspurity-galaxy + Galaxy wrapper version: 0.0.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/computational-metabolomics/mspurity-galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 9 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: apollo + Conda version: 4.2.13 + Date of first commit of the suite: '2020-06-29' + Description: Access an Apollo instance from Galaxy + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - create_account + - feat_from_gff3 + - create_or_update + - delete_features + - delete_organism + - export + - fetch_jbrowse + - iframe + - list_organism + Galaxy wrapper id: apollo + Galaxy wrapper owner: gga + Galaxy wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo + Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 3600 + No. of tool users (5 years) (usegalaxy.org): 6 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3606 + No. of tool users (all time) (usegalaxy.eu): 3760 + No. of tool users (all time) (usegalaxy.org): 6 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3766 + Source: https://github.com/galaxy-genome-annotation/python-apollo + Status: To update + Tool usage (5 years) (usegalaxy.eu): 883 + Tool usage (5 years) (usegalaxy.org): 4 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 887 + Tool usage (all time) (usegalaxy.eu): 911 + Tool usage (all time) (usegalaxy.org): 4 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 915 + ToolShed categories: + - Web Services + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 9 + Tools available on UseGalaxy.eu: 9 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 9 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 9 + UseGalaxy.eu: 9 + UseGalaxy.no: 9 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: askocli + Conda version: '0.5' + Date of first commit of the suite: '2017-08-11' + Description: Galaxy tools allowing to interact with a remote AskOmics server.AskOmics + is a visual SPARQL query builder for RDF database.https://github.com/askomics/ + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - askomics_integrate + Galaxy wrapper id: askomics + Galaxy wrapper owner: gga + Galaxy wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics + Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/askomics/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Web Services + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python-chado + Conda version: 2.3.9 + Date of first commit of the suite: '2018-11-05' + Description: Galaxy tools allowing to load data into a remote Chado database.Chado + is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - analysis_add_analysis + - analysis_delete_analyses + - analysis_get_analyses + - export_export_fasta + - export_export_gbk + - export_export_gff3 + - expression_add_biomaterial + - expression_add_expression + - expression_delete_all_biomaterials + - expression_delete_biomaterials + - expression_get_biomaterials + - feature_delete_features + - feature_get_features + - feature_load_fasta + - feature_load_featureprops + - feature_load_gff + - feature_load_go + - load_blast + - load_interpro + - organism_add_organism + - organism_delete_all_organisms + - organism_delete_organisms + - organism_get_organisms + - phylogeny_gene_families + - phylogeny_gene_order + - phylogeny_load_tree + Galaxy wrapper id: chado + Galaxy wrapper owner: gga + Galaxy wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado + Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/galaxy-genome-annotation/python-chado + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Web Services + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: genoboo + Conda version: 0.4.16 + Date of first commit of the suite: '2023-04-07' + Description: Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - genenotebook_build + Galaxy wrapper id: genenotebook + Galaxy wrapper owner: gga + Galaxy wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook + Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook + Galaxy wrapper version: 0.4.16 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1 + Source: https://genenotebook.github.io + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Web Services + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2016-11-08' + Description: A tool allowing to export a JBrowse dataset into a JBrowse docker container + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - jbrowse_to_container + Galaxy wrapper id: jbrowse + Galaxy wrapper owner: gga + Galaxy wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse + Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://jbrowse.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Web Services + ToolShed id: jbrowse_to_container + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-11-01' + Description: Tool for annotation of repeats from unassembled shotgun reads. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - repeatexplorer_clustering + Galaxy wrapper id: repeatexplorer2 + Galaxy wrapper owner: gga + Galaxy wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 + Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 + Galaxy wrapper version: 2.3.8 + No. of tool users (5 years) (usegalaxy.eu): 95 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 95 + No. of tool users (all time) (usegalaxy.eu): 95 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 95 + Source: https://github.com/repeatexplorer/repex_tarean + Status: To update + Tool usage (5 years) (usegalaxy.eu): 38 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 38 + Tool usage (all time) (usegalaxy.eu): 38 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 38 + ToolShed categories: + - Genome annotation + ToolShed id: repeatexplorer2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python-tripal + Conda version: 3.2.1 + Date of first commit of the suite: '2018-06-20' + Description: Galaxy tools allowing to load data into a remote Tripal server.Tripal + is a toolkit for construction of online biological (genetics, genomics, breeding, + etc), community database,and is a member of the GMOD family of tools. Tripal provides + by default integration with the GMOD Chado database schema and Drupal, a popular + Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - analysis_add_analysis + - analysis_get_analyses + - analysis_load_blast + - analysis_load_fasta + - analysis_load_gff3 + - analysis_load_go + - analysis_load_interpro + - analysis_sync + - db_index + - db_populate_mviews + - entity_publish + - expression_add_biomaterial + - expression_add_expression + - expression_delete_biomaterials + - expression_get_biomaterials + - expression_sync_biomaterials + - feature_delete_orphans + - feature_sync + - organism_add_organism + - organism_get_organisms + - organism_sync + - phylogeny_sync + Galaxy wrapper id: tripal + Galaxy wrapper owner: gga + Galaxy wrapper parsed folder: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal + Galaxy wrapper source: https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/galaxy-genome-annotation/python-tripal + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Web Services + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2018-09-05' + Description: OPLS-DA Contrasts of Univariate Results + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - w4mcorcov + Galaxy wrapper id: w4mcorcov + Galaxy wrapper owner: eschen42 + Galaxy wrapper parsed folder: https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov + Galaxy wrapper source: https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master + Galaxy wrapper version: 0.98.18 + No. of tool users (5 years) (usegalaxy.eu): 238 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 10 + No. of tool users (5 years) - all main servers: 248 + No. of tool users (all time) (usegalaxy.eu): 375 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 10 + No. of tool users (all time) - all main servers: 385 + Source: https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 2 + Tool usage (5 years) - all main servers: 12 + Tool usage (all time) (usegalaxy.eu): 10 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 2 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - Metabolomics + ToolShed id: w4mcorcov + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2019-09-26' + Description: Filter W4M data by values or metadata + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - w4mclassfilter + Galaxy wrapper id: w4mclassfilter + Galaxy wrapper owner: eschen42 + Galaxy wrapper parsed folder: https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter + Galaxy wrapper source: https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master + Galaxy wrapper version: 0.98.19 + No. of tool users (5 years) (usegalaxy.eu): 2370 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1482 + No. of tool users (5 years) - all main servers: 3852 + No. of tool users (all time) (usegalaxy.eu): 2836 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1509 + No. of tool users (all time) - all main servers: 4345 + Source: https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 13 + Tool usage (all time) (usegalaxy.eu): 10 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 14 + ToolShed categories: + - Metabolomics + ToolShed id: w4mclassfilter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: coreutils + Conda version: '8.25' + Date of first commit of the suite: '2018-08-06' + Description: Join positive- and negative-mode W4M datasets + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - w4mjoinpn + Galaxy wrapper id: w4mjoinpn + Galaxy wrapper owner: eschen42 + Galaxy wrapper parsed folder: https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn + Galaxy wrapper source: https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master + Galaxy wrapper version: 0.98.2 + No. of tool users (5 years) (usegalaxy.eu): 150 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 7 + No. of tool users (5 years) - all main servers: 157 + No. of tool users (all time) (usegalaxy.eu): 171 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 7 + No. of tool users (all time) - all main servers: 178 + Source: https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 2 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 2 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Metabolomics + ToolShed id: w4mjoinpn + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2019-01-22' + Description: Automatic thresholding + EDAM operation: + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM operation (no superclasses): + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM topic: + - Imaging + - Software engineering + - Literature and language + EDAM topic (no superclasses): + - Imaging + - Software engineering + - Literature and language + Galaxy tool ids: + - ip_threshold + Galaxy wrapper id: 2d_auto_threshold + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ + Galaxy wrapper version: 0.18.1 + No. of tool users (5 years) (usegalaxy.eu): 1434 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 305 + No. of tool users (5 years) - all main servers: 1739 + No. of tool users (all time) (usegalaxy.eu): 6746 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 305 + No. of tool users (all time) - all main servers: 7051 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 120 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 11 + Tool usage (5 years) - all main servers: 131 + Tool usage (all time) (usegalaxy.eu): 122 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 11 + Tool usage (all time) - all main servers: 133 + ToolShed categories: + - Imaging + ToolShed id: 2d_auto_threshold + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: scikit-image + bio.tool description: Scikit-image contains image processing algorithms for SciPy, + including IO, morphology, filtering, warping, color manipulation, object detection, + etc. + bio.tool id: scikit-image + bio.tool ids: + - scikit-image + bio.tool name: scikit-image +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2019-01-08' + Description: 2D feature extraction + EDAM operation: + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM operation (no superclasses): + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM topic: + - Imaging + - Software engineering + - Literature and language + EDAM topic (no superclasses): + - Imaging + - Software engineering + - Literature and language + Galaxy tool ids: + - ip_2d_feature_extraction + Galaxy wrapper id: 2d_feature_extraction + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ + Galaxy wrapper version: 0.18.1 + No. of tool users (5 years) (usegalaxy.eu): 1156 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 121 + No. of tool users (5 years) - all main servers: 1277 + No. of tool users (all time) (usegalaxy.eu): 13842 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 121 + No. of tool users (all time) - all main servers: 13963 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 40 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 44 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 46 + ToolShed categories: + - Imaging + ToolShed id: 2d_feature_extraction + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: scikit-image + bio.tool description: Scikit-image contains image processing algorithms for SciPy, + including IO, morphology, filtering, warping, color manipulation, object detection, + etc. + bio.tool id: scikit-image + bio.tool ids: + - scikit-image + bio.tool name: scikit-image +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2019-07-19' + Description: filter segmentation by rules + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_2d_filter_segmentation_by_features + Galaxy wrapper id: 2d_filter_segmentation_by_features + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ + Galaxy wrapper version: 0.0.1-4 + No. of tool users (5 years) (usegalaxy.eu): 591 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 119 + No. of tool users (5 years) - all main servers: 710 + No. of tool users (all time) (usegalaxy.eu): 6863 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 119 + No. of tool users (all time) - all main servers: 6982 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 38 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 41 + Tool usage (all time) (usegalaxy.eu): 40 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 43 + ToolShed categories: + - Imaging + ToolShed id: 2d_filter_segmentation_by_features + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2019-07-23' + Description: 2d histogram equalization + EDAM operation: + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM operation (no superclasses): + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM topic: + - Imaging + - Software engineering + - Literature and language + EDAM topic (no superclasses): + - Imaging + - Software engineering + - Literature and language + Galaxy tool ids: + - ip_histogram_equalization + Galaxy wrapper id: 2d_histogram_equalization + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ + Galaxy wrapper version: 0.18.1 + No. of tool users (5 years) (usegalaxy.eu): 762 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 230 + No. of tool users (5 years) - all main servers: 992 + No. of tool users (all time) (usegalaxy.eu): 782 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 230 + No. of tool users (all time) - all main servers: 1012 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 100 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 14 + Tool usage (5 years) - all main servers: 114 + Tool usage (all time) (usegalaxy.eu): 101 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 14 + Tool usage (all time) - all main servers: 115 + ToolShed categories: + - Imaging + ToolShed id: 2d_histogram_equalization + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: scikit-image + bio.tool description: Scikit-image contains image processing algorithms for SciPy, + including IO, morphology, filtering, warping, color manipulation, object detection, + etc. + bio.tool id: scikit-image + bio.tool ids: + - scikit-image + bio.tool name: scikit-image +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: scipy + Conda version: null + Date of first commit of the suite: '2019-01-22' + Description: 2d simple filter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_filter_standard + Galaxy wrapper id: 2d_simple_filter + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ + Galaxy wrapper version: 1.12.0 + No. of tool users (5 years) (usegalaxy.eu): 948 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 153 + No. of tool users (5 years) - all main servers: 1101 + No. of tool users (all time) (usegalaxy.eu): 6261 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 153 + No. of tool users (all time) - all main servers: 6414 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 98 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 13 + Tool usage (5 years) - all main servers: 111 + Tool usage (all time) (usegalaxy.eu): 100 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 13 + Tool usage (all time) - all main servers: 113 + ToolShed categories: + - Imaging + ToolShed id: 2d_simple_filter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: scipy + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: medpy + Conda version: 0.4.0 + Date of first commit of the suite: '2018-12-04' + Description: Anisotropic image diffusion + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_anisotropic_diffusion + Galaxy wrapper id: anisotropic_diffusion + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ + Galaxy wrapper version: 0.4.0 + No. of tool users (5 years) (usegalaxy.eu): 36 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 36 + No. of tool users (all time) (usegalaxy.eu): 41 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 41 + Source: https://github.com/bmcv + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: anisotropic_diffusion + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2024-07-12' + Description: Background removal filters using scikit-image + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - background_removal + Galaxy wrapper id: background_removal + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tools/background_removal + Galaxy wrapper version: 0.24.0 + No. of tool users (5 years) (usegalaxy.eu): 5 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5 + No. of tool users (all time) (usegalaxy.eu): 5 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Imaging + ToolShed id: background_removal + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: bftools + Conda version: 6.7.0 + Date of first commit of the suite: '2019-07-22' + Description: Convert image + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_convertimage + Galaxy wrapper id: bfconvert + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ + Galaxy wrapper version: 6.7.0 + No. of tool users (5 years) (usegalaxy.eu): 1635 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 334 + No. of tool users (5 years) - all main servers: 1969 + No. of tool users (all time) (usegalaxy.eu): 1671 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 334 + No. of tool users (all time) - all main servers: 2005 + Source: https://github.com/bmcv + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 123 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 21 + Tool usage (5 years) - all main servers: 144 + Tool usage (all time) (usegalaxy.eu): 124 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 21 + Tool usage (all time) - all main servers: 145 + ToolShed categories: + - Imaging + - Convert Formats + ToolShed id: bfconvert + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: python-bioformats + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2017-02-11' + Description: Binary 2 label image + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_binary_to_labelimage + Galaxy wrapper id: binary2labelimage + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ + Galaxy wrapper version: '0.5' + No. of tool users (5 years) (usegalaxy.eu): 401 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 188 + No. of tool users (5 years) - all main servers: 589 + No. of tool users (all time) (usegalaxy.eu): 1385 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 188 + No. of tool users (all time) - all main servers: 1573 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 87 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 9 + Tool usage (5 years) - all main servers: 96 + Tool usage (all time) (usegalaxy.eu): 88 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 9 + Tool usage (all time) - all main servers: 97 + ToolShed categories: + - Imaging + ToolShed id: binary2labelimage + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2017-10-30' + Description: Binary Image to Points + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_binaryimage_to_points + Galaxy wrapper id: binaryimage2points + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ + Galaxy wrapper version: 0.1-2 + No. of tool users (5 years) (usegalaxy.eu): 24 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 24 + No. of tool users (all time) (usegalaxy.eu): 29 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 29 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Imaging + ToolShed id: binaryimage2points + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-11-02' + Description: Convert image to OME-Zarr + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bf2raw + Galaxy wrapper id: bioformats2raw + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw + Galaxy wrapper version: 0.7.0 + No. of tool users (5 years) (usegalaxy.eu): 61 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 61 + No. of tool users (all time) (usegalaxy.eu): 61 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 61 + Source: https://github.com/Euro-BioImaging + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Imaging + - Convert Formats + ToolShed id: bioformats2raw + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2024-09-30' + Description: Color-deconvolution methods + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_color_deconvolution + Galaxy wrapper id: color_deconvolution + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ + Galaxy wrapper version: '0.8' + No. of tool users (5 years) (usegalaxy.eu): 15 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 15 + No. of tool users (all time) (usegalaxy.eu): 16 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 16 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Imaging + ToolShed id: color_deconvolution + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: networkx + Conda version: null + Date of first commit of the suite: '2024-03-12' + Description: Colorize label map + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - colorize_labels + Galaxy wrapper id: colorize_labels + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels + Galaxy wrapper version: 3.2.1 + No. of tool users (5 years) (usegalaxy.eu): 40 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 40 + No. of tool users (all time) (usegalaxy.eu): 40 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 40 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: colorize_labels + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2017-10-30' + Description: Concatenate images + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_concat_channels + Galaxy wrapper id: concat_channels + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ + Galaxy wrapper version: 0.3-1 + No. of tool users (5 years) (usegalaxy.eu): 76 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 76 + No. of tool users (all time) (usegalaxy.eu): 82 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 82 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - Imaging + ToolShed id: concat_channels + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2019-01-08' + Description: Coordinates of ROI + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_coordinates_of_roi + Galaxy wrapper id: coordinates_of_roi + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ + Galaxy wrapper version: 0.0.4-2 + No. of tool users (5 years) (usegalaxy.eu): 16077 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 16077 + No. of tool users (all time) (usegalaxy.eu): 16547 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 16547 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Imaging + ToolShed id: coordinates_of_roi + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2019-01-08' + Description: Count Objects + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_count_objects + Galaxy wrapper id: count_objects + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ + Galaxy wrapper version: 0.0.5-2 + No. of tool users (5 years) (usegalaxy.eu): 314 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 129 + No. of tool users (5 years) - all main servers: 443 + No. of tool users (all time) (usegalaxy.eu): 326 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 129 + No. of tool users (all time) - all main servers: 455 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 73 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 6 + Tool usage (5 years) - all main servers: 79 + Tool usage (all time) (usegalaxy.eu): 75 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 6 + Tool usage (all time) - all main servers: 81 + ToolShed categories: + - Imaging + ToolShed id: count_objects + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2021-07-22' + Description: Polynomial curve fitting to data points + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_curve_fitting + Galaxy wrapper id: curve_fitting + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ + Galaxy wrapper version: 0.0.3-2 + No. of tool users (5 years) (usegalaxy.eu): 12 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 12 + No. of tool users (all time) (usegalaxy.eu): 12 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 12 + Source: https://github.com/BMCV/galaxy-image-analysis + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: curve_fitting + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2017-10-30' + Description: Detection Visualization + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_detection_viz + Galaxy wrapper id: detection_viz + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ + Galaxy wrapper version: 0.3-2 + No. of tool users (5 years) (usegalaxy.eu): 43 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 43 + No. of tool users (all time) (usegalaxy.eu): 48 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 48 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Imaging + ToolShed id: detection_viz + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: bftools + Conda version: 6.7.0 + Date of first commit of the suite: '2019-07-19' + Description: Extracts image metadata + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_imageinfo + Galaxy wrapper id: image_info + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ + Galaxy wrapper version: 5.7.1 + No. of tool users (5 years) (usegalaxy.eu): 273 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 153 + No. of tool users (5 years) - all main servers: 426 + No. of tool users (all time) (usegalaxy.eu): 659 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 153 + No. of tool users (all time) - all main servers: 812 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 101 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 15 + Tool usage (5 years) - all main servers: 116 + Tool usage (all time) (usegalaxy.eu): 102 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 15 + Tool usage (all time) - all main servers: 117 + ToolShed categories: + - Imaging + ToolShed id: image_info + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: python-bioformats + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2024-03-09' + Description: Process images using arithmetic expressions + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - image_math + Galaxy wrapper id: image_math + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math + Galaxy wrapper version: 1.26.4 + No. of tool users (5 years) (usegalaxy.eu): 58 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 58 + No. of tool users (all time) (usegalaxy.eu): 58 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 58 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: image_math + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2020-12-29' + Description: Intensity-based Image Registration + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_image_registration + Galaxy wrapper id: image_registration_affine + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ + Galaxy wrapper version: 0.0.3-2 + No. of tool users (5 years) (usegalaxy.eu): 16 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 16 + No. of tool users (all time) (usegalaxy.eu): 16 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 16 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Imaging + ToolShed id: image_registration_affine + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pandas + Conda version: null + Date of first commit of the suite: '2019-03-08' + Description: Flip coordinate axes + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - imagecoordinates_flipaxis + Galaxy wrapper id: imagecoordinates_flipaxis + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ + Galaxy wrapper version: 0.1-2 + No. of tool users (5 years) (usegalaxy.eu): 21409 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 21409 + No. of tool users (all time) (usegalaxy.eu): 21849 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 21849 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 10 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - Imaging + ToolShed id: imagecoordinates_flipaxis + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2024-03-13' + Description: Convert label map to binary image + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - label_to_binary + Galaxy wrapper id: label_to_binary + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ + Galaxy wrapper version: 1.26.4 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Imaging + ToolShed id: label_to_binary + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2017-10-30' + Description: Label Image to Points + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_labelimage_to_points + Galaxy wrapper id: labelimage2points + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ + Galaxy wrapper version: 0.2-2 + No. of tool users (5 years) (usegalaxy.eu): 34 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 34 + No. of tool users (all time) (usegalaxy.eu): 38 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 38 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: labelimage2points + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2019-02-04' + Description: Landmark Registration + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_landmark_registration + Galaxy wrapper id: landmark_registration + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ + Galaxy wrapper version: 0.1.0-2 + No. of tool users (5 years) (usegalaxy.eu): 887 + No. of tool users (5 years) (usegalaxy.org): 4 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 891 + No. of tool users (all time) (usegalaxy.eu): 927 + No. of tool users (all time) (usegalaxy.org): 4 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 931 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 13 + Tool usage (5 years) (usegalaxy.org): 3 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 16 + Tool usage (all time) (usegalaxy.eu): 15 + Tool usage (all time) (usegalaxy.org): 3 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 18 + ToolShed categories: + - Imaging + ToolShed id: landmark_registration + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mahotas + Conda version: null + Date of first commit of the suite: '2024-09-30' + Description: Compute image features using mahotas. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_mahotas_features + Galaxy wrapper id: mahotas_features + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ + Galaxy wrapper version: 0.7-2 + No. of tool users (5 years) (usegalaxy.eu): 39 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 39 + No. of tool users (all time) (usegalaxy.eu): 44 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 44 + Source: https://github.com/luispedro/mahotas + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Imaging + ToolShed id: mahotas_features + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: mahotas-feature-computation + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2019-01-08' + Description: Merge Neighbours in Label Image + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_merge_neighbours_in_label + Galaxy wrapper id: mergeneighboursinlabelimage + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage + Galaxy wrapper version: 0.3-2 + No. of tool users (5 years) (usegalaxy.eu): 18 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 18 + No. of tool users (all time) (usegalaxy.eu): 25 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 25 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Imaging + ToolShed id: mergeneighboursinlabelimage + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scipy + Conda version: null + Date of first commit of the suite: '2024-03-08' + Description: Apply morphological operations to images + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - morphological_operations + Galaxy wrapper id: morphological_operations + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations + Galaxy wrapper version: 1.12.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Imaging + ToolShed id: morphological_operations + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: scipy + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: orientationpy + Conda version: 0.2.0.4 + Date of first commit of the suite: '2024-03-12' + Description: Compute image orientation + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - orientationpy + Galaxy wrapper id: orientationpy + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy + Galaxy wrapper version: 0.2.0.4 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bmcv + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Imaging + ToolShed id: orientationpy + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: orientationj + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2022-02-26' + Description: Overlay two images + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_overlay_images + Galaxy wrapper id: overlay_images + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ + Galaxy wrapper version: 0.0.4 + No. of tool users (5 years) (usegalaxy.eu): 149 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 18 + No. of tool users (5 years) - all main servers: 167 + No. of tool users (all time) (usegalaxy.eu): 149 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 18 + No. of tool users (all time) - all main servers: 167 + Source: https://github.com/BMCV/galaxy-image-analysis + Status: To update + Tool usage (5 years) (usegalaxy.eu): 31 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 32 + Tool usage (all time) (usegalaxy.eu): 31 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 32 + ToolShed categories: + - Imaging + ToolShed id: overlay_images + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2017-10-30' + Description: Permutates axes + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_permutate_axis + Galaxy wrapper id: permutate_axis + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ + Galaxy wrapper version: 0.2-2 + No. of tool users (5 years) (usegalaxy.eu): 36 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 36 + No. of tool users (all time) (usegalaxy.eu): 42 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 42 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: permutate_axis + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: plant-seg + Conda version: null + Date of first commit of the suite: '2024-06-19' + Description: Tool for cell instance aware segmentation in densely packed 3D volumetric + images + EDAM operation: + - Network analysis + - Quantification + - Microscope image visualisation + EDAM operation (no superclasses): + - Network analysis + - Quantification + - Microscope image visualisation + EDAM topic: + - Plant biology + - Bioimaging + - Light microscopy + - Machine learning + - Electron microscopy + EDAM topic (no superclasses): + - Plant biology + - Bioimaging + - Light microscopy + - Machine learning + - Electron microscopy + Galaxy tool ids: + - plantseg + Galaxy wrapper id: plantseg + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ + Galaxy wrapper version: 1.8.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Imaging + ToolShed id: plantseg + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Accurate and Versatile 3D Segmentation of Plant Tissues at + Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in + densely packed 3D volumetric images. The pipeline uses a two stages segmentation + strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell + tissue acquired with confocal and light sheet microscopy. Pre-trained models are + provided. + bio.tool id: plantseg + bio.tool ids: + - plantseg + bio.tool name: PlantSeg +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2018-11-20' + Description: Points to label image + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_points_to_label + Galaxy wrapper id: points2labelimage + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ + Galaxy wrapper version: '0.4' + No. of tool users (5 years) (usegalaxy.eu): 33 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 33 + No. of tool users (all time) (usegalaxy.eu): 33 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 33 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: points2labelimage + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2021-07-22' + Description: Association of points in consecutive frames + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_points_association_nn + Galaxy wrapper id: points_association_nn + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ + Galaxy wrapper version: 0.0.3-2 + No. of tool users (5 years) (usegalaxy.eu): 29 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 29 + No. of tool users (all time) (usegalaxy.eu): 29 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 29 + Source: https://github.com/BMCV/galaxy-image-analysis + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Imaging + ToolShed id: points_association_nn + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2018-12-07' + Description: Projective transformation + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_projective_transformation + Galaxy wrapper id: projective_transformation + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 40 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 40 + No. of tool users (all time) (usegalaxy.eu): 86 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 86 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Imaging + ToolShed id: projective_transformation + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2018-12-07' + Description: Projective transformation of ROIs defined by pixel (point) coordinates + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_projective_transformation_points + Galaxy wrapper id: projective_transformation_points + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ + Galaxy wrapper version: 0.1.1 + No. of tool users (5 years) (usegalaxy.eu): 20858 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 20858 + No. of tool users (all time) (usegalaxy.eu): 21444 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 21444 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 14 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 14 + Tool usage (all time) (usegalaxy.eu): 18 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 18 + ToolShed categories: + - Imaging + ToolShed id: projective_transformation_points + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2024-04-25' + Description: Convert single-channel to multi-channel image + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - repeat_channels + Galaxy wrapper id: repeat_channels + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ + Galaxy wrapper version: 1.26.4 + No. of tool users (5 years) (usegalaxy.eu): 5 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5 + No. of tool users (all time) (usegalaxy.eu): 5 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Imaging + ToolShed id: repeat_channels + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-11-12' + Description: Perform segmentation region-based fitting of overlapping ellipses + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Cell biology + - Biomedical science + - Imaging + EDAM topic (no superclasses): + - Cell biology + - Biomedical science + - Imaging + Galaxy tool ids: + - rfove + Galaxy wrapper id: rfove + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ + Galaxy wrapper version: 2023.11.12 + No. of tool users (5 years) (usegalaxy.eu): 15 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 15 + No. of tool users (all time) (usegalaxy.eu): 15 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 15 + Source: https://sites.google.com/site/costaspanagiotakis/research/cs + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - Imaging + ToolShed id: rfove + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: RFOVE (Region-based Fitting of Overlapping Ellipses and its + Application to Cells Segmentation) is a MATLAB script for performing image segmentation + on cells. + bio.tool id: rfove + bio.tool ids: + - rfove + bio.tool name: RFOVE +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2018-12-07' + Description: Scale image + EDAM operation: + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM operation (no superclasses): + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM topic: + - Imaging + - Software engineering + - Literature and language + EDAM topic (no superclasses): + - Imaging + - Software engineering + - Literature and language + Galaxy tool ids: + - ip_scale_image + Galaxy wrapper id: scale_image + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ + Galaxy wrapper version: 0.18.3 + No. of tool users (5 years) (usegalaxy.eu): 477 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 477 + No. of tool users (all time) (usegalaxy.eu): 520 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 520 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 13 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 13 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 16 + ToolShed categories: + - Imaging + ToolShed id: scale_image + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: scikit-image + bio.tool description: Scikit-image contains image processing algorithms for SciPy, + including IO, morphology, filtering, warping, color manipulation, object detection, + etc. + bio.tool id: scikit-image + bio.tool ids: + - scikit-image + bio.tool name: scikit-image +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: segmetrics + Conda version: '1.5' + Date of first commit of the suite: '2022-10-07' + Description: Image segmentation and object detection performance measures + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_segmetrics + Galaxy wrapper id: segmetrics + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ + Galaxy wrapper version: '1.4' + No. of tool users (5 years) (usegalaxy.eu): 7 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7 + No. of tool users (all time) (usegalaxy.eu): 7 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: segmetrics + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: segmetrics + bio.tool description: Image segmentation and object detection performance measures + bio.tool id: segmetrics + bio.tool ids: + - segmetrics + bio.tool name: SegMetrics +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2017-10-30' + Description: Slice image + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_slice_image + Galaxy wrapper id: slice_image + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ + Galaxy wrapper version: 0.3-4 + No. of tool users (5 years) (usegalaxy.eu): 96 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 4 + No. of tool users (5 years) - all main servers: 100 + No. of tool users (all time) (usegalaxy.eu): 103 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 4 + No. of tool users (all time) - all main servers: 107 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Imaging + ToolShed id: slice_image + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2018-12-11' + Description: Split Labelmaps + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_split_labelmap + Galaxy wrapper id: split_labelmap + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ + Galaxy wrapper version: 0.2-3 + No. of tool users (5 years) (usegalaxy.eu): 44 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 44 + No. of tool users (all time) (usegalaxy.eu): 51 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 51 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Imaging + ToolShed id: split_labelmap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: giatools + Conda version: 0.3.1 + Date of first commit of the suite: '2021-07-20' + Description: Spot detection in 2D image sequence + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Bioinformatics + EDAM topic (no superclasses): + - Imaging + - Bioinformatics + Galaxy tool ids: + - ip_spot_detection_2d + Galaxy wrapper id: spot_detection_2d + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 16 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 16 + No. of tool users (all time) (usegalaxy.eu): 16 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 16 + Source: https://github.com/BMCV/galaxy-image-analysis + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Imaging + ToolShed id: spot_detection_2d + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Galaxy Image Analysis is mainly developed by the Biomedical + Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide + tools for image analysis and image processing for the Galaxy platform. + bio.tool id: galaxy_image_analysis + bio.tool ids: + - galaxy_image_analysis + bio.tool name: Galaxy Image Analysis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: superdsm + Conda version: 0.4.0 + Date of first commit of the suite: '2023-07-05' + Description: Globally optimal segmentation method based on superadditivity and deformable + shape models for cell nuclei in fluorescence microscopy images + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_superdsm + Galaxy wrapper id: superdsm + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 26 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 26 + No. of tool users (all time) (usegalaxy.eu): 26 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 26 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Imaging + ToolShed id: superdsm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: superdsm + bio.tool description: SuperDSM is a globally optimal segmentation method based on + superadditivity and deformable shape models for cell nuclei in fluorescence microscopy + images and beyond. + bio.tool id: superdsm + bio.tool ids: + - superdsm + bio.tool name: SuperDSM +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: unzip + Conda version: null + Date of first commit of the suite: '2019-08-01' + Description: Unzip file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - unzip + Galaxy wrapper id: unzip + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ + Galaxy wrapper version: '6.0' + No. of tool users (5 years) (usegalaxy.eu): 6942 + No. of tool users (5 years) (usegalaxy.org): 1 + No. of tool users (5 years) (usegalaxy.org.au): 2461 + No. of tool users (5 years) - all main servers: 9404 + No. of tool users (all time) (usegalaxy.eu): 7024 + No. of tool users (all time) (usegalaxy.org): 1 + No. of tool users (all time) (usegalaxy.org.au): 2461 + No. of tool users (all time) - all main servers: 9486 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1345 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 266 + Tool usage (5 years) - all main servers: 1612 + Tool usage (all time) (usegalaxy.eu): 1356 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 266 + Tool usage (all time) - all main servers: 1623 + ToolShed categories: + - Convert Formats + ToolShed id: unzip + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: visceral-evaluatesegmentation + Conda version: 2015.07.03 + Date of first commit of the suite: '2024-09-30' + Description: Visceral Project - Evaluate Segmentation Tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_visceral_evaluatesegmentation + Galaxy wrapper id: visceral_evaluatesegmentation + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation + Galaxy wrapper version: 0.5-2 + No. of tool users (5 years) (usegalaxy.eu): 20 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 20 + No. of tool users (all time) (usegalaxy.eu): 25 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 25 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Imaging + ToolShed id: visceral_evaluatesegmentation + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: evaluatesegmentation-tool + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2024-03-09' + Description: Compute Voronoi tesselation + EDAM operation: + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM operation (no superclasses): + - Image analysis + - Image annotation + - Visualisation + - Data handling + EDAM topic: + - Imaging + - Software engineering + - Literature and language + EDAM topic (no superclasses): + - Imaging + - Software engineering + - Literature and language + Galaxy tool ids: + - voronoi_tessellation + Galaxy wrapper id: voronoi_tessellation + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation + Galaxy wrapper version: 0.22.0 + No. of tool users (5 years) (usegalaxy.eu): 43 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 43 + No. of tool users (all time) (usegalaxy.eu): 43 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 43 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 3 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Imaging + ToolShed id: voronoi_tesselation + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: scikit-image + bio.tool description: Scikit-image contains image processing algorithms for SciPy, + including IO, morphology, filtering, warping, color manipulation, object detection, + etc. + bio.tool id: scikit-image + bio.tool ids: + - scikit-image + bio.tool name: scikit-image +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-image + Conda version: null + Date of first commit of the suite: '2017-10-30' + Description: WSI Extract Top View + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ip_wsi_extract_top_view + Galaxy wrapper id: wsi_extract_top_view + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view + Galaxy wrapper source: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ + Galaxy wrapper version: 0.2-2 + No. of tool users (5 years) (usegalaxy.eu): 32 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 32 + No. of tool users (all time) (usegalaxy.eu): 38 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 38 + Source: https://github.com/bmcv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Imaging + ToolShed id: wsi_extract_top_view + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: lastz + Conda version: 1.04.22 + Date of first commit of the suite: '2024-04-30' + Description: Galaxy wrapper for the batching Lastz runs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - batched_lastz + Galaxy wrapper id: batched_lastz + Galaxy wrapper owner: richard-burhans + Galaxy wrapper parsed folder: https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz + Galaxy wrapper source: https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz + Galaxy wrapper version: 1.04.22 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 123 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 123 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 123 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 123 + Source: https://github.com/galaxyproject/KegAlign + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 5 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 5 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Next Gen Mappers + ToolShed id: batched_lastz + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: kegalign-full + Conda version: 0.1.2.7 + Date of first commit of the suite: '2024-08-29' + Description: A Scalable GPU System for Pairwise Whole Genome Alignments based on + LASTZ's seed-filter-extend paradigm. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - kegalign + Galaxy wrapper id: kegalign + Galaxy wrapper owner: richard-burhans + Galaxy wrapper parsed folder: https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign + Galaxy wrapper source: https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign + Galaxy wrapper version: 0.1.2.7 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 5 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 5 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5 + Source: https://github.com/galaxyproject/KegAlign + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Next Gen Mappers + ToolShed id: kegalign + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-08-19' + Description: Eukaryotic Genome Annotation Pipeline - External (EGAPx) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ncbi_egapx + Galaxy wrapper id: ncbi_egapx + Galaxy wrapper owner: richard-burhans + Galaxy wrapper parsed folder: https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx + Galaxy wrapper source: https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx + Galaxy wrapper version: 0.2-alpha + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 15 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 15 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 15 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 15 + Source: https://github.com/ncbi/egapx + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 6 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 6 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Genome annotation + ToolShed id: ncbi_egapx + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-02-23' + Description: FCS-adaptor detects adaptor and vector contamination in genome sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ncbi_fcs_adaptor + Galaxy wrapper id: ncbi_fcs_adaptor + Galaxy wrapper owner: richard-burhans + Galaxy wrapper parsed folder: https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor + Galaxy wrapper source: https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor + Galaxy wrapper version: 0.5.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 842 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 842 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 842 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 842 + Source: https://github.com/ncbi/fcs + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 93 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 93 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 93 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 93 + ToolShed categories: + - Sequence Analysis + ToolShed id: ncbi_fcs_adaptor + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: segalign-galaxy + Conda version: 0.1.2.7 + Date of first commit of the suite: '2024-04-18' + Description: A Scalable GPU System for Pairwise Whole Genome Alignments based on + LASTZ's seed-filter-extend paradigm. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - segalign + Galaxy wrapper id: segalign + Galaxy wrapper owner: richard-burhans + Galaxy wrapper parsed folder: https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign + Galaxy wrapper source: https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign + Galaxy wrapper version: 0.1.2.7 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 252 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 252 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 252 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 252 + Source: https://github.com/gsneha26/SegAlign + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 47 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 47 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 47 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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qiime2__alignment__mafft + - qiime2__alignment__mafft_add + - qiime2__alignment__mask + Galaxy wrapper id: suite_qiime2__alignment + Galaxy wrapper owner: q2d2 + Galaxy wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + Galaxy wrapper version: 2024.5.0+q2galaxy.2024.5.0 + No. of tool users (5 years) (usegalaxy.eu): 249 + No. of tool users (5 years) (usegalaxy.org): 16 + No. of tool users (5 years) (usegalaxy.org.au): 102 + No. of tool users (5 years) - all main servers: 367 + No. of tool users (all time) (usegalaxy.eu): 249 + No. of tool users (all time) (usegalaxy.org): 16 + No. of tool users (all time) (usegalaxy.org.au): 102 + No. of tool users (all time) - all main servers: 367 + Source: https://github.com/qiime2/q2-alignment + Status: To update + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 10 + Tool usage (5 years) (usegalaxy.org.au): 16 + Tool usage (5 years) - 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qiime2__composition__add_pseudocount + - qiime2__composition__ancom + - qiime2__composition__ancombc + - qiime2__composition__da_barplot + - qiime2__composition__tabulate + Galaxy wrapper id: suite_qiime2__composition + Galaxy wrapper owner: q2d2 + Galaxy wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + Galaxy wrapper version: 2024.5.0+q2galaxy.2024.5.0 + No. of tool users (5 years) (usegalaxy.eu): 117 + No. of tool users (5 years) (usegalaxy.org): 84 + No. of tool users (5 years) (usegalaxy.org.au): 161 + No. of tool users (5 years) - all main servers: 362 + No. of tool users (all time) (usegalaxy.eu): 117 + No. of tool users (all time) (usegalaxy.org): 84 + No. of tool users (all time) (usegalaxy.org.au): 161 + No. of tool users (all time) - all main servers: 362 + Source: https://github.com/qiime2/q2-composition + Status: To update + Tool usage (5 years) (usegalaxy.eu): 41 + Tool usage (5 years) (usegalaxy.org): 24 + Tool usage (5 years) (usegalaxy.org.au): 13 + Tool usage (5 years) - 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qiime2__cutadapt__demux_paired + - qiime2__cutadapt__demux_single + - qiime2__cutadapt__trim_paired + - qiime2__cutadapt__trim_single + Galaxy wrapper id: suite_qiime2__cutadapt + Galaxy wrapper owner: q2d2 + Galaxy wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + Galaxy wrapper version: 2024.5.0+q2galaxy.2024.5.0 + No. of tool users (5 years) (usegalaxy.eu): 217 + No. of tool users (5 years) (usegalaxy.org): 42 + No. of tool users (5 years) (usegalaxy.org.au): 96 + No. of tool users (5 years) - all main servers: 355 + No. of tool users (all time) (usegalaxy.eu): 217 + No. of tool users (all time) (usegalaxy.org): 42 + No. of tool users (all time) (usegalaxy.org.au): 96 + No. of tool users (all time) - all main servers: 355 + Source: https://github.com/qiime2/q2-cutadapt + Status: To update + Tool usage (5 years) (usegalaxy.eu): 47 + Tool usage (5 years) (usegalaxy.org): 20 + Tool usage (5 years) (usegalaxy.org.au): 12 + Tool usage (5 years) - 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qiime2__dada2__denoise_ccs + - qiime2__dada2__denoise_paired + - qiime2__dada2__denoise_pyro + - qiime2__dada2__denoise_single + Galaxy wrapper id: suite_qiime2__dada2 + Galaxy wrapper owner: q2d2 + Galaxy wrapper parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + Galaxy wrapper source: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + Galaxy wrapper version: 2024.5.0+q2galaxy.2024.5.0 + No. of tool users (5 years) (usegalaxy.eu): 721 + No. of tool users (5 years) (usegalaxy.org): 350 + No. of tool users (5 years) (usegalaxy.org.au): 214 + No. of tool users (5 years) - all main servers: 1285 + No. of tool users (all time) (usegalaxy.eu): 721 + No. of tool users (all time) (usegalaxy.org): 350 + No. of tool users (all time) (usegalaxy.org.au): 214 + No. of tool users (all time) - all main servers: 1285 + Source: http://benjjneb.github.io/dada2/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 160 + Tool usage (5 years) (usegalaxy.org): 91 + Tool usage (5 years) (usegalaxy.org.au): 35 + Tool usage (5 years) - 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fasta_concatenate0 + Galaxy wrapper id: fasta_concatenate_by_species + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 39695 + No. of tool users (5 years) (usegalaxy.org): 13660 + No. of tool users (5 years) (usegalaxy.org.au): 1521 + No. of tool users (5 years) - all main servers: 54876 + No. of tool users (all time) (usegalaxy.eu): 39742 + No. of tool users (all time) (usegalaxy.org): 19007 + No. of tool users (all time) (usegalaxy.org.au): 1603 + No. of tool users (all time) - all main servers: 60352 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 242 + Tool usage (5 years) (usegalaxy.org): 600 + Tool usage (5 years) (usegalaxy.org.au): 92 + Tool usage (5 years) - 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fasta_filter_by_length + Galaxy wrapper id: fasta_filter_by_length + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length + Galaxy wrapper version: '1.2' + No. of tool users (5 years) (usegalaxy.eu): 47494 + No. of tool users (5 years) (usegalaxy.org): 50663 + No. of tool users (5 years) (usegalaxy.org.au): 3919 + No. of tool users (5 years) - all main servers: 102076 + No. of tool users (all time) (usegalaxy.eu): 51924 + No. of tool users (all time) (usegalaxy.org): 101663 + No. of tool users (all time) (usegalaxy.org.au): 5601 + No. of tool users (all time) - all main servers: 159188 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 889 + Tool usage (5 years) (usegalaxy.org): 1488 + Tool usage (5 years) (usegalaxy.org.au): 241 + Tool usage (5 years) - all main servers: 2618 + Tool usage (all time) (usegalaxy.eu): 997 + Tool usage (all time) (usegalaxy.org): 3742 + Tool usage (all time) (usegalaxy.org.au): 276 + Tool usage (all time) - all main servers: 5015 + ToolShed categories: + - Fasta Manipulation + ToolShed id: fasta_filter_by_length + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2014-05-19' + Description: FASTA-to-Tabular converter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fasta2tab + Galaxy wrapper id: fasta_to_tabular + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular + Galaxy wrapper version: 1.1.1 + No. of tool users (5 years) (usegalaxy.eu): 108876 + No. of tool users (5 years) (usegalaxy.org): 82527 + No. of tool users (5 years) (usegalaxy.org.au): 5711 + No. of tool users (5 years) - all main servers: 197114 + No. of tool users (all time) (usegalaxy.eu): 113638 + No. of tool users (all time) (usegalaxy.org): 192112 + No. of tool users (all time) (usegalaxy.org.au): 7649 + No. of tool users (all time) - all main servers: 313399 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1572 + Tool usage (5 years) (usegalaxy.org): 2209 + Tool usage (5 years) (usegalaxy.org.au): 275 + Tool usage (5 years) - all main servers: 4056 + Tool usage (all time) (usegalaxy.eu): 1793 + Tool usage (all time) (usegalaxy.org): 8565 + Tool usage (all time) (usegalaxy.org.au): 334 + Tool usage (all time) - all main servers: 10692 + ToolShed categories: + - Fasta Manipulation + ToolShed id: fasta_to_tabular + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2014-01-27' + Description: FASTQ Quality Trimmer by sliding window + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_quality_trimmer + Galaxy wrapper id: fastq_trimmer_by_quality + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 4881 + No. of tool users (5 years) (usegalaxy.org): 29458 + No. of tool users (5 years) (usegalaxy.org.au): 2171 + No. of tool users (5 years) - all main servers: 36510 + No. of tool users (all time) (usegalaxy.eu): 6165 + No. of tool users (all time) (usegalaxy.org): 99179 + No. of tool users (all time) (usegalaxy.org.au): 2678 + No. of tool users (all time) - all main servers: 108022 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 859 + Tool usage (5 years) (usegalaxy.org): 3455 + Tool usage (5 years) (usegalaxy.org.au): 259 + Tool usage (5 years) - all main servers: 4573 + Tool usage (all time) (usegalaxy.eu): 967 + Tool usage (all time) (usegalaxy.org): 11369 + Tool usage (all time) (usegalaxy.org.au): 338 + Tool usage (all time) - 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featureCoverage1 + Galaxy wrapper id: featurecounter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter + Galaxy wrapper version: 2.0.0 + No. of tool users (5 years) (usegalaxy.eu): 22308 + No. of tool users (5 years) (usegalaxy.org): 350 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 22658 + No. of tool users (all time) (usegalaxy.eu): 22388 + No. of tool users (all time) (usegalaxy.org): 13711 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 36099 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 54 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 70 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 349 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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all main servers: 330 + ToolShed categories: + - Sequence Analysis + - Variant Analysis + ToolShed id: windowsplitter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2013-09-25' + Description: Plotting tool for multiple series and graph types + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - XY_Plot_1 + Galaxy wrapper id: xy_plot + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 4490 + No. of tool users (5 years) (usegalaxy.org): 6120 + No. of tool users (5 years) (usegalaxy.org.au): 2033 + No. of tool users (5 years) - all main servers: 12643 + No. of tool users (all time) (usegalaxy.eu): 6169 + No. of tool users (all time) (usegalaxy.org): 15516 + No. of tool users (all time) (usegalaxy.org.au): 2212 + No. of tool users (all time) - all main servers: 23897 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 768 + Tool usage (5 years) (usegalaxy.org): 1921 + Tool usage (5 years) (usegalaxy.org.au): 556 + Tool usage (5 years) - all main servers: 3245 + Tool usage (all time) (usegalaxy.eu): 889 + Tool usage (all time) (usegalaxy.org): 3653 + Tool usage (all time) (usegalaxy.org.au): 590 + Tool usage (all time) - all main servers: 5132 + ToolShed categories: + - Graphics + - Statistics + ToolShed id: xy_plot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 1 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bx-python + Conda version: 0.13.0 + Date of first commit of the suite: '2014-04-01' + Description: Base Coverage of all intervals + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gops_basecoverage_1 + Galaxy wrapper id: basecoverage + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 226 + No. of tool users (5 years) (usegalaxy.org): 2615 + No. of tool users (5 years) (usegalaxy.org.au): 482 + No. of tool users (5 years) - all main servers: 3323 + No. of tool users (all time) (usegalaxy.eu): 308 + No. of tool users (all time) (usegalaxy.org): 45557 + No. of tool users (all time) (usegalaxy.org.au): 522 + No. of tool users (all time) - all main servers: 46387 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 27 + Tool usage (5 years) (usegalaxy.org): 302 + Tool usage (5 years) (usegalaxy.org.au): 32 + Tool usage (5 years) - 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gops_cluster_1 + Galaxy wrapper id: cluster + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 513 + No. of tool users (5 years) (usegalaxy.org): 2406 + No. of tool users (5 years) (usegalaxy.org.au): 1353 + No. of tool users (5 years) - all main servers: 4272 + No. of tool users (all time) (usegalaxy.eu): 813 + No. of tool users (all time) (usegalaxy.org): 30579 + No. of tool users (all time) (usegalaxy.org.au): 1393 + No. of tool users (all time) - all main servers: 32785 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 18 + Tool usage (5 years) (usegalaxy.org): 156 + Tool usage (5 years) (usegalaxy.org.au): 17 + Tool usage (5 years) - all main servers: 191 + Tool usage (all time) (usegalaxy.eu): 35 + Tool usage (all time) (usegalaxy.org): 1547 + Tool usage (all time) (usegalaxy.org.au): 20 + Tool usage (all time) - all main servers: 1602 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: cluster + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bx-python + Conda version: 0.13.0 + Date of first commit of the suite: '2014-04-01' + Description: Complement intervals of a dataset + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gops_complement_1 + Galaxy wrapper id: complement + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 187 + No. of tool users (5 years) (usegalaxy.org): 495 + No. of tool users (5 years) (usegalaxy.org.au): 405 + No. of tool users (5 years) - all main servers: 1087 + No. of tool users (all time) (usegalaxy.eu): 233 + No. of tool users (all time) (usegalaxy.org): 4810 + No. of tool users (all time) (usegalaxy.org.au): 451 + No. of tool users (all time) - all main servers: 5494 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 15 + Tool usage (5 years) (usegalaxy.org): 165 + Tool usage (5 years) (usegalaxy.org.au): 7 + Tool usage (5 years) - 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gops_concat_1 + Galaxy wrapper id: concat + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 575128 + No. of tool users (5 years) (usegalaxy.org): 43420 + No. of tool users (5 years) (usegalaxy.org.au): 19330 + No. of tool users (5 years) - all main servers: 637878 + No. of tool users (all time) (usegalaxy.eu): 575441 + No. of tool users (all time) (usegalaxy.org): 85345 + No. of tool users (all time) (usegalaxy.org.au): 19418 + No. of tool users (all time) - all main servers: 680204 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 694 + Tool usage (5 years) (usegalaxy.org): 629 + Tool usage (5 years) (usegalaxy.org.au): 104 + Tool usage (5 years) - 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gops_coverage_1 + Galaxy wrapper id: coverage + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 1560 + No. of tool users (5 years) (usegalaxy.org): 4328 + No. of tool users (5 years) (usegalaxy.org.au): 283 + No. of tool users (5 years) - all main servers: 6171 + No. of tool users (all time) (usegalaxy.eu): 1725 + No. of tool users (all time) (usegalaxy.org): 44209 + No. of tool users (all time) (usegalaxy.org.au): 316 + No. of tool users (all time) - all main servers: 46250 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 43 + Tool usage (5 years) (usegalaxy.org): 193 + Tool usage (5 years) (usegalaxy.org.au): 16 + Tool usage (5 years) - 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flanking_features_1 + Galaxy wrapper id: flanking_features + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features + Galaxy wrapper version: 4.0.1 + No. of tool users (5 years) (usegalaxy.eu): 589 + No. of tool users (5 years) (usegalaxy.org): 2445 + No. of tool users (5 years) (usegalaxy.org.au): 1214 + No. of tool users (5 years) - all main servers: 4248 + No. of tool users (all time) (usegalaxy.eu): 731 + No. of tool users (all time) (usegalaxy.org): 32847 + No. of tool users (all time) (usegalaxy.org.au): 1294 + No. of tool users (all time) - all main servers: 34872 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 51 + Tool usage (5 years) (usegalaxy.org): 304 + Tool usage (5 years) (usegalaxy.org.au): 15 + Tool usage (5 years) - all main servers: 370 + Tool usage (all time) (usegalaxy.eu): 63 + Tool usage (all time) (usegalaxy.org): 2549 + Tool usage (all time) (usegalaxy.org.au): 22 + Tool usage (all time) - all main servers: 2634 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: flanking_features + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bx-python + Conda version: 0.13.0 + Date of first commit of the suite: '2014-04-01' + Description: Get flanks returns flanking region/s for every gene + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - get_flanks1 + Galaxy wrapper id: get_flanks + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 3768 + No. of tool users (5 years) (usegalaxy.org): 9350 + No. of tool users (5 years) (usegalaxy.org.au): 787 + No. of tool users (5 years) - all main servers: 13905 + No. of tool users (all time) (usegalaxy.eu): 325011 + No. of tool users (all time) (usegalaxy.org): 242043 + No. of tool users (all time) (usegalaxy.org.au): 1070 + No. of tool users (all time) - all main servers: 568124 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1462 + Tool usage (5 years) (usegalaxy.org): 2201 + Tool usage (5 years) (usegalaxy.org.au): 119 + Tool usage (5 years) - all main servers: 3782 + Tool usage (all time) (usegalaxy.eu): 2044 + Tool usage (all time) (usegalaxy.org): 6583 + Tool usage (all time) (usegalaxy.org.au): 146 + Tool usage (all time) - all main servers: 8773 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: get_flanks + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bx-python + Conda version: 0.13.0 + Date of first commit of the suite: '2014-04-01' + Description: Intersect the intervals of two datasets + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gops_intersect_1 + Galaxy wrapper id: intersect + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 20472 + No. of tool users (5 years) (usegalaxy.org): 45587 + No. of tool users (5 years) (usegalaxy.org.au): 6087 + No. of tool users (5 years) - all main servers: 72146 + No. of tool users (all time) (usegalaxy.eu): 349984 + No. of tool users (all time) (usegalaxy.org): 778988 + No. of tool users (all time) (usegalaxy.org.au): 7417 + No. of tool users (all time) - all main servers: 1136389 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2351 + Tool usage (5 years) (usegalaxy.org): 4359 + Tool usage (5 years) (usegalaxy.org.au): 484 + Tool usage (5 years) - all main servers: 7194 + Tool usage (all time) (usegalaxy.eu): 3007 + Tool usage (all time) (usegalaxy.org): 14116 + Tool usage (all time) (usegalaxy.org.au): 561 + Tool usage (all time) - all main servers: 17684 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: intersect + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bx-python + Conda version: 0.13.0 + Date of first commit of the suite: '2014-04-01' + Description: Join the intervals of two datasets side-by-side + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gops_join_1 + Galaxy wrapper id: join + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 15624 + No. of tool users (5 years) (usegalaxy.org): 52317 + No. of tool users (5 years) (usegalaxy.org.au): 1329 + No. of tool users (5 years) - all main servers: 69270 + No. of tool users (all time) (usegalaxy.eu): 330820 + No. of tool users (all time) (usegalaxy.org): 513688 + No. of tool users (all time) (usegalaxy.org.au): 1645 + No. of tool users (all time) - all main servers: 846153 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1864 + Tool usage (5 years) (usegalaxy.org): 10198 + Tool usage (5 years) (usegalaxy.org.au): 213 + Tool usage (5 years) - all main servers: 12275 + Tool usage (all time) (usegalaxy.eu): 2438 + Tool usage (all time) (usegalaxy.org): 39421 + Tool usage (all time) (usegalaxy.org.au): 289 + Tool usage (all time) - all main servers: 42148 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: join + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bx-python + Conda version: 0.13.0 + Date of first commit of the suite: '2014-04-01' + Description: Merge the overlapping intervals of a dataset + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gops_merge_1 + Galaxy wrapper id: merge + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 565922 + No. of tool users (5 years) (usegalaxy.org): 45844 + No. of tool users (5 years) (usegalaxy.org.au): 19828 + No. of tool users (5 years) - all main servers: 631594 + No. of tool users (all time) (usegalaxy.eu): 566630 + No. of tool users (all time) (usegalaxy.org): 107523 + No. of tool users (all time) (usegalaxy.org.au): 19994 + No. of tool users (all time) - all main servers: 694147 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 418 + Tool usage (5 years) (usegalaxy.org): 671 + Tool usage (5 years) (usegalaxy.org.au): 100 + Tool usage (5 years) - 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gops_subtract_1 + Galaxy wrapper id: subtract + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 566512 + No. of tool users (5 years) (usegalaxy.org): 49985 + No. of tool users (5 years) (usegalaxy.org.au): 20648 + No. of tool users (5 years) - all main servers: 637145 + No. of tool users (all time) (usegalaxy.eu): 567199 + No. of tool users (all time) (usegalaxy.org): 184650 + No. of tool users (all time) (usegalaxy.org.au): 20897 + No. of tool users (all time) - all main servers: 772746 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 410 + Tool usage (5 years) (usegalaxy.org): 1473 + Tool usage (5 years) (usegalaxy.org.au): 155 + Tool usage (5 years) - 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subtract_query1 + Galaxy wrapper id: subtract_query + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 1178 + No. of tool users (5 years) (usegalaxy.org): 3169 + No. of tool users (5 years) (usegalaxy.org.au): 799 + No. of tool users (5 years) - all main servers: 5146 + No. of tool users (all time) (usegalaxy.eu): 1450 + No. of tool users (all time) (usegalaxy.org): 40539 + No. of tool users (all time) (usegalaxy.org.au): 950 + No. of tool users (all time) - all main servers: 42939 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 124 + Tool usage (5 years) (usegalaxy.org): 636 + Tool usage (5 years) (usegalaxy.org.au): 26 + Tool usage (5 years) - 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tables_arithmetic_operations + Galaxy wrapper id: tables_arithmetic_operations + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 2188 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2188 + No. of tool users (all time) (usegalaxy.eu): 2220 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2220 + Source: https://github.com/galaxyproject/gops + Status: To update + Tool usage (5 years) (usegalaxy.eu): 33 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 33 + Tool usage (all time) (usegalaxy.eu): 38 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 38 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: tables_arithmetic_operations + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2013-09-25' + Description: FunDO human genes associated with disease terms + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hgv_funDo + Galaxy wrapper id: hgv_fundo + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 145 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 145 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 1794 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1794 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 33 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 33 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 397 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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hgv_hilbertvis + Galaxy wrapper id: hgv_hilbertvis + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 119 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 119 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 265 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 265 + Source: https://www.ebi.ac.uk/huber-srv/hilbert/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 16 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 16 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 60 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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hgv_snpFreq + Galaxy wrapper id: snpfreq + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 35 + No. of tool users (5 years) (usegalaxy.org): 307 + No. of tool users (5 years) (usegalaxy.org.au): 227 + No. of tool users (5 years) - all main servers: 569 + No. of tool users (all time) (usegalaxy.eu): 44 + No. of tool users (all time) (usegalaxy.org): 649 + No. of tool users (all time) (usegalaxy.org.au): 260 + No. of tool users (all time) - all main servers: 953 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 68 + Tool usage (5 years) (usegalaxy.org.au): 16 + Tool usage (5 years) - all main servers: 94 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 181 + Tool usage (all time) (usegalaxy.org.au): 23 + Tool usage (all time) - 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find_diag_hits + Galaxy wrapper id: find_diag_hits + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 62 + No. of tool users (5 years) (usegalaxy.org): 3 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 65 + No. of tool users (all time) (usegalaxy.eu): 70 + No. of tool users (all time) (usegalaxy.org): 1787 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1857 + Source: https://bitbucket.org/natefoo/taxonomy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 204 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 216 + ToolShed categories: + - Metagenomics + ToolShed id: find_diag_hits + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: taxonomy + Conda version: 0.10.0 + Date of first commit of the suite: '2014-01-27' + Description: Fetch taxonomic representation + EDAM operation: + - Database search + - ID mapping + EDAM operation (no superclasses): + - Database search + - ID mapping + EDAM topic: + - Taxonomy + EDAM topic (no superclasses): + - Taxonomy + Galaxy tool ids: + - Fetch Taxonomic Ranks + Galaxy wrapper id: gi2taxonomy + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy + Galaxy wrapper version: 1.1.1 + No. of tool users (5 years) (usegalaxy.eu): 490 + No. of tool users (5 years) (usegalaxy.org): 127 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 617 + No. of tool users (all time) (usegalaxy.eu): 682 + No. of tool users (all time) (usegalaxy.org): 14058 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 14740 + Source: https://bitbucket.org/natefoo/taxonomy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 74 + Tool usage (5 years) (usegalaxy.org): 20 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 94 + Tool usage (all time) (usegalaxy.eu): 109 + Tool usage (all time) (usegalaxy.org): 1798 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1907 + ToolShed categories: + - Metagenomics + ToolShed id: gi2taxonomy + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: The tool fetches taxonomic information for a list of sequence + identifiers (i.e. GI numbers, as used by the National Center for Biotechnology + Information (NCBI). + bio.tool id: gi2taxonomy + bio.tool ids: + - gi2taxonomy + bio.tool name: gi2taxonomy +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: gawk + Conda version: null + Date of first commit of the suite: '2015-08-05' + Description: Convert Kraken output to Galaxy taxonomy data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - Kraken2Tax + Galaxy wrapper id: kraken2tax + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ + Galaxy wrapper version: 1.2+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 23008 + No. of tool users (5 years) (usegalaxy.org): 16194 + No. of tool users (5 years) (usegalaxy.org.au): 14898 + No. of tool users (5 years) - all main servers: 54100 + No. of tool users (all time) (usegalaxy.eu): 23014 + No. of tool users (all time) (usegalaxy.org): 24490 + No. of tool users (all time) (usegalaxy.org.au): 14898 + No. of tool users (all time) - all main servers: 62402 + Source: https://bitbucket.org/natefoo/taxonomy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1060 + Tool usage (5 years) (usegalaxy.org): 1719 + Tool usage (5 years) (usegalaxy.org.au): 436 + Tool usage (5 years) - all main servers: 3215 + Tool usage (all time) (usegalaxy.eu): 1061 + Tool usage (all time) (usegalaxy.org): 2168 + Tool usage (all time) (usegalaxy.org.au): 436 + Tool usage (all time) - all main servers: 3665 + ToolShed categories: + - Metagenomics + ToolShed id: kraken2tax + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: taxonomy + Conda version: 0.10.0 + Date of first commit of the suite: '2014-01-27' + Description: Find lowest diagnostic rank + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - lca1 + Galaxy wrapper id: lca_wrapper + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 89 + No. of tool users (5 years) (usegalaxy.org): 118 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 207 + No. of tool users (all time) (usegalaxy.eu): 137 + No. of tool users (all time) (usegalaxy.org): 6136 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6273 + Source: https://bitbucket.org/natefoo/taxonomy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 15 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 19 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 1112 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1132 + ToolShed categories: + - Metagenomics + ToolShed id: lca_wrapper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: taxonomy + Conda version: 0.10.0 + Date of first commit of the suite: '2014-01-27' + Description: Poisson two-sample test + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - poisson2test + Galaxy wrapper id: poisson2test + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 112 + No. of tool users (5 years) (usegalaxy.org): 4 + No. of tool users (5 years) (usegalaxy.org.au): 320 + No. of tool users (5 years) - all main servers: 436 + No. of tool users (all time) (usegalaxy.eu): 120 + No. of tool users (all time) (usegalaxy.org): 562 + No. of tool users (all time) (usegalaxy.org.au): 347 + No. of tool users (all time) - all main servers: 1029 + Source: https://bitbucket.org/natefoo/taxonomy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 7 + Tool usage (5 years) - all main servers: 24 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 140 + Tool usage (all time) (usegalaxy.org.au): 8 + Tool usage (all time) - all main servers: 164 + ToolShed categories: + - Statistics + - Metagenomics + ToolShed id: poisson2test + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: taxonomy + Conda version: 0.10.0 + Date of first commit of the suite: '2014-01-27' + Description: Draw phylogeny + EDAM operation: + - Phylogenetic tree visualisation + EDAM operation (no superclasses): + - Phylogenetic tree visualisation + EDAM topic: + - Phylogenomics + EDAM topic (no superclasses): + - Phylogenomics + Galaxy tool ids: + - Draw_phylogram + Galaxy wrapper id: t2ps + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 411 + No. of tool users (5 years) (usegalaxy.org): 102 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 513 + No. of tool users (all time) (usegalaxy.eu): 472 + No. of tool users (all time) (usegalaxy.org): 7952 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8424 + Source: https://bitbucket.org/natefoo/taxonomy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 68 + Tool usage (5 years) (usegalaxy.org): 13 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 81 + Tool usage (all time) (usegalaxy.eu): 90 + Tool usage (all time) (usegalaxy.org): 1240 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1330 + ToolShed categories: + - Metagenomics + ToolShed id: t2ps + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: '"Given taxonomy representation (produced by *Fetch taxonomic + representation* tool) this utility produces a graphical representations of phylogenetic + tree in PDF format." - Galaxy tool wrapper' + bio.tool id: t2ps + bio.tool ids: + - t2ps + bio.tool name: Draw phylogeny +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: taxonomy + Conda version: 0.10.0 + Date of first commit of the suite: '2014-01-27' + Description: Summarize taxonomy + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - t2t_report + Galaxy wrapper id: t2t_report + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 927 + No. of tool users (5 years) (usegalaxy.org): 130 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1057 + No. of tool users (all time) (usegalaxy.eu): 959 + No. of tool users (all time) (usegalaxy.org): 7194 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8153 + Source: https://bitbucket.org/natefoo/taxonomy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 65 + Tool usage (5 years) (usegalaxy.org): 18 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 83 + Tool usage (all time) (usegalaxy.eu): 78 + Tool usage (all time) (usegalaxy.org): 1143 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1221 + ToolShed categories: + - Metagenomics + ToolShed id: t2t_report + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: echo + Conda version: null + Date of first commit of the suite: '2013-11-24' + Description: Annotate VCF using custom/user-defined annotations + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcftools_annotate + Galaxy wrapper id: vcftools_annotate + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 155 + No. of tool users (5 years) (usegalaxy.org): 1853 + No. of tool users (5 years) (usegalaxy.org.au): 144 + No. of tool users (5 years) - all main servers: 2152 + No. of tool users (all time) (usegalaxy.eu): 192 + No. of tool users (all time) (usegalaxy.org): 3943 + No. of tool users (all time) (usegalaxy.org.au): 156 + No. of tool users (all time) - all main servers: 4291 + Source: https://vcftools.github.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 81 + Tool usage (5 years) (usegalaxy.org): 581 + Tool usage (5 years) (usegalaxy.org.au): 13 + Tool usage (5 years) - all main servers: 675 + Tool usage (all time) (usegalaxy.eu): 90 + Tool usage (all time) (usegalaxy.org): 1280 + Tool usage (all time) (usegalaxy.org.au): 16 + Tool usage (all time) - all main servers: 1386 + ToolShed categories: + - Variant Analysis + ToolShed id: vcftools_annotate + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: tabix + Conda version: '1.11' + Date of first commit of the suite: '2013-11-24' + Description: Compare VCF files to get overlap and uniqueness statistics + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcftools_compare + Galaxy wrapper id: vcftools_compare + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 440 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 440 + No. of tool users (all time) (usegalaxy.eu): 594 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 16 + No. of tool users (all time) - all main servers: 610 + Source: https://vcftools.github.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 127 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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vcftools_merge + Galaxy wrapper id: vcftools_merge + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge + Galaxy wrapper version: 0.1.11 + No. of tool users (5 years) (usegalaxy.eu): 817 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 93 + No. of tool users (5 years) - all main servers: 910 + No. of tool users (all time) (usegalaxy.eu): 1084 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 448 + No. of tool users (all time) - all main servers: 1532 + Source: https://vcftools.github.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 244 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 44 + Tool usage (5 years) - 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vcftools_slice + Galaxy wrapper id: vcftools_slice + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 410 + No. of tool users (5 years) (usegalaxy.org): 6261 + No. of tool users (5 years) (usegalaxy.org.au): 127 + No. of tool users (5 years) - all main servers: 6798 + No. of tool users (all time) (usegalaxy.eu): 423 + No. of tool users (all time) (usegalaxy.org): 8115 + No. of tool users (all time) (usegalaxy.org.au): 157 + No. of tool users (all time) - all main servers: 8695 + Source: https://vcftools.github.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 56 + Tool usage (5 years) (usegalaxy.org): 133 + Tool usage (5 years) (usegalaxy.org.au): 10 + Tool usage (5 years) - 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vcftools_subset + Galaxy wrapper id: vcftools_subset + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset + Galaxy wrapper source: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 134 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 120 + No. of tool users (5 years) - all main servers: 254 + No. of tool users (all time) (usegalaxy.eu): 142 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 142 + No. of tool users (all time) - all main servers: 284 + Source: https://vcftools.github.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 46 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 12 + Tool usage (5 years) - 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all main servers: 84 + ToolShed categories: + - Convert Formats + ToolShed id: 10x_bamtofastq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2018-10-24' + Description: Aggregate and filter alignment metrics of individual clusters, like + the output of graphclust_align_cluster. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - 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graphclust_align_cluster + Galaxy wrapper id: AlignCluster + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 189 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 189 + No. of tool users (all time) (usegalaxy.eu): 3094 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3094 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 23 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 23 + Tool usage (all time) (usegalaxy.eu): 25 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 25 + ToolShed categories: + - RNA + ToolShed id: graphclust_align_cluster + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2016-12-15' + Description: Determines consensus motives for sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cmFinder + Galaxy wrapper id: CMFinder + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder + Galaxy wrapper version: '0.4' + No. of tool users (5 years) (usegalaxy.eu): 25532 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 25532 + No. of tool users (all time) (usegalaxy.eu): 50045 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 50045 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 45 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 45 + Tool usage (all time) (usegalaxy.eu): 57 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 57 + ToolShed categories: + - RNA + ToolShed id: graphclust_cmfinder + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2017-01-21' + Description: Post-processing. Redundant clusters are merged and instances that belong + to multiple clusters are assigned unambiguously. For every pair of clusters, the + relative overlap (i.e. the fraction of instances that occur in both clusters) + is computed and clusters are merged if the overlap exceeds 50%. instances that + occur in both clusters) is computed and clusters are merged if the overlap exceeds + 50%. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - glob_report + Galaxy wrapper id: CollectResults + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults + Galaxy wrapper version: '0.5' + No. of tool users (5 years) (usegalaxy.eu): 1119 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1119 + No. of tool users (all time) (usegalaxy.eu): 2115 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2115 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 50 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 50 + Tool usage (all time) (usegalaxy.eu): 62 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 62 + ToolShed categories: + - RNA + ToolShed id: graphclust_postprocessing + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2018-10-25' + Description: Redundant GraphClust clusters are merged and instances that belong + to multiple clusters are assigned unambiguously. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - graphclust_glob_report_no_align + Galaxy wrapper id: CollectResultsNoAlign + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign + Galaxy wrapper version: '0.5' + No. of tool users (5 years) (usegalaxy.eu): 37 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 37 + No. of tool users (all time) (usegalaxy.eu): 108 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 108 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - RNA + ToolShed id: graphclust_postprocessing_no_align + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2016-12-15' + Description: Second step of GraphClust + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gspan + Galaxy wrapper id: GSPAN + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN + Galaxy wrapper version: '0.4' + No. of tool users (5 years) (usegalaxy.eu): 80 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 80 + No. of tool users (all time) (usegalaxy.eu): 150 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 150 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 18 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 18 + Tool usage (all time) (usegalaxy.eu): 23 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 23 + ToolShed categories: + - RNA + ToolShed id: graphclust_fasta_to_gspan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2016-12-15' + Description: MLocARNA computes a multiple sequence-structure alignment of RNA sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - locarna_best_subtree + Galaxy wrapper id: LocARNAGraphClust + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust + Galaxy wrapper version: '0.4' + No. of tool users (5 years) (usegalaxy.eu): 25572 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 25572 + No. of tool users (all time) (usegalaxy.eu): 50177 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 50177 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 45 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 45 + Tool usage (all time) (usegalaxy.eu): 57 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 57 + ToolShed categories: + - RNA + ToolShed id: graphclust_mlocarna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2016-12-15' + Description: Produces an explicit sparse feature encoding and copmutes global feature + index and returns top dense sets. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - NSPDK_candidateClust + - nspdk_sparse + Galaxy wrapper id: NSPDK + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK + Galaxy wrapper version: 9.2.3.1 + No. of tool users (5 years) (usegalaxy.eu): 3210 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3210 + No. of tool users (all time) (usegalaxy.eu): 62854 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 62854 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 96 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 96 + Tool usage (all time) (usegalaxy.eu): 124 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 124 + ToolShed categories: + - RNA + ToolShed id: graphclust_nspdk + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.no: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: seaborn + Conda version: null + Date of first commit of the suite: '2017-02-22' + Description: Plotting results for GraphClust + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - motifFinderPlot + Galaxy wrapper id: Plotting + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting + Galaxy wrapper source: https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting + Galaxy wrapper version: '0.4' + No. of tool users (5 years) (usegalaxy.eu): 45 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 45 + No. of tool users (all time) (usegalaxy.eu): 71 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 71 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 10 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 10 + ToolShed categories: + - RNA + ToolShed id: graphclust_motif_finder_plot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2016-12-15' + Description: This tool prepares files for locarna step. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - 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preproc + Galaxy wrapper id: Preprocessing + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust + Galaxy wrapper version: '0.5' + No. of tool users (5 years) (usegalaxy.eu): 1116 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1116 + No. of tool users (all time) (usegalaxy.eu): 1897 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1897 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 57 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 57 + Tool usage (all time) (usegalaxy.eu): 71 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 71 + ToolShed categories: + - RNA + ToolShed id: graphclust_preprocessing + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphclust-wrappers + Conda version: 0.6.0 + Date of first commit of the suite: '2017-05-18' + Description: Convert RNA structure to GSPAN graphs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - structure_to_gspan + Galaxy wrapper id: Structure_GSPAN + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN + Galaxy wrapper source: https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN + Galaxy wrapper version: '0.4' + No. of tool users (5 years) (usegalaxy.eu): 991 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 991 + No. of tool users (all time) (usegalaxy.eu): 3060 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3060 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 50 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 50 + Tool usage (all time) (usegalaxy.eu): 62 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 62 + ToolShed categories: + - RNA + ToolShed id: structure_to_gspan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: agat + Conda version: 1.4.1 + Date of first commit of the suite: '2023-05-22' + Description: GTF/GFF analysis toolkit + EDAM operation: + - Data handling + - Genome annotation + EDAM operation (no superclasses): + - Data handling + - Genome annotation + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - agat + Galaxy wrapper id: agat + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/agat + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/agat + Galaxy wrapper version: 1.4.0 + No. of tool users (5 years) (usegalaxy.eu): 1436 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 119 + No. of tool users (5 years) - all main servers: 1555 + No. of tool users (all time) (usegalaxy.eu): 1436 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 119 + No. of tool users (all time) - all main servers: 1555 + Source: https://github.com/NBISweden/AGAT + Status: To update + Tool usage (5 years) (usegalaxy.eu): 244 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 10 + Tool usage (5 years) - all main servers: 254 + Tool usage (all time) (usegalaxy.eu): 244 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 10 + Tool usage (all time) - all main servers: 254 + ToolShed categories: + - Convert Formats + - Statistics + - Fasta Manipulation + ToolShed id: agat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Another Gff Analysis Toolkit (AGAT)Suite of tools to handle + gene annotations in any GTF/GFF format. + bio.tool id: agat + bio.tool ids: + - agat + bio.tool name: AGAT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: antismash + Conda version: 7.1.0 + Date of first commit of the suite: '2015-02-28' + Description: Antismash allows the genome-wide identification, annotation and analysis + of secondary metabolite biosynthesis gene clusters + EDAM operation: + - Sequence clustering + - Gene prediction + - Differential gene expression analysis + EDAM operation (no superclasses): + - Sequence clustering + - Gene prediction + - Differential gene expression analysis + EDAM topic: + - Molecular interactions, pathways and networks + - Gene and protein families + EDAM topic (no superclasses): + - Molecular interactions, pathways and networks + - Gene and protein families + Galaxy tool ids: + - antismash + Galaxy wrapper id: antismash + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/antismash + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash + Galaxy wrapper version: 6.1.1 + No. of tool users (5 years) (usegalaxy.eu): 15949 + No. of tool users (5 years) (usegalaxy.org): 5113 + No. of tool users (5 years) (usegalaxy.org.au): 6043 + No. of tool users (5 years) - 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antismash + bio.tool name: antiSMASH +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: atactk + Conda version: 0.1.9 + Date of first commit of the suite: '2018-06-20' + Description: Trim adapters from paired-end HTS reads. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - atactk_trim_adapters + Galaxy wrapper id: atactk_trim_adapters + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters + Galaxy wrapper source: https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters + Galaxy wrapper version: 0.1.6 + No. of tool users (5 years) (usegalaxy.eu): 232 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 232 + No. of tool users (all time) (usegalaxy.eu): 279 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 279 + Source: https://github.com/ParkerLab/atactk/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 62 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 62 + Tool usage (all time) (usegalaxy.eu): 72 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 72 + ToolShed categories: + - Fastq Manipulation + ToolShed id: atactk_trim_adapters + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: augustus + Conda version: 3.5.0 + Date of first commit of the suite: '2015-02-28' + Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - augustus + Galaxy wrapper id: augustus + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/augustus + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/augustus + Galaxy wrapper version: 3.1.0 + No. of tool users (5 years) (usegalaxy.eu): 10109 + No. of tool users (5 years) (usegalaxy.org): 12573 + No. of tool users (5 years) (usegalaxy.org.au): 5274 + No. of tool users (5 years) - all main servers: 27956 + No. of tool users (all time) (usegalaxy.eu): 11052 + No. of tool users (all time) (usegalaxy.org): 12573 + No. of tool users (all time) (usegalaxy.org.au): 5274 + No. of tool users (all time) - all main servers: 28899 + Source: http://bioinf.uni-greifswald.de/augustus/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1378 + Tool usage (5 years) (usegalaxy.org): 2206 + Tool usage (5 years) (usegalaxy.org.au): 369 + Tool usage (5 years) - all main servers: 3953 + Tool usage (all time) (usegalaxy.eu): 1509 + Tool usage (all time) (usegalaxy.org): 2206 + Tool usage (all time) (usegalaxy.org.au): 369 + Tool usage (all time) - all main servers: 4084 + ToolShed categories: + - Sequence Analysis + ToolShed id: augustus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bamhash + Conda version: '1.1' + Date of first commit of the suite: '2015-09-17' + Description: Hash BAM and FASTQ files to verify data integrity + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bamhash + Galaxy wrapper id: bamhash + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/bamhash + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/bamhash + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 158 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 158 + No. of tool users (all time) (usegalaxy.eu): 181 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 181 + Source: https://github.com/DecodeGenetics/BamHash + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 40 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 40 + Tool usage (all time) (usegalaxy.eu): 44 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 44 + ToolShed categories: + - Sequence Analysis + ToolShed id: bamhash + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pysam + Conda version: 0.22.1 + Date of first commit of the suite: '2016-06-11' + Description: Paired End randomer aware duplicate removal algorithm + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - barcode_collapse + Galaxy wrapper id: barcode_collapse + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/YeoLab/gscripts + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - RNA + - Sequence Analysis + ToolShed id: barcode_collapse + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ucsc_tools + Conda version: null + Date of first commit of the suite: '2015-06-04' + Description: Convert from bigWig to bedGraph format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bigwig_to_bedgraph + Galaxy wrapper id: bigwig_to_bedgraph + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 5769 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5769 + No. of tool users (all time) (usegalaxy.eu): 6802 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 3 + No. of tool users (all time) - all main servers: 6805 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 567 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 567 + Tool usage (all time) (usegalaxy.eu): 650 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 651 + ToolShed categories: + - Convert Formats + ToolShed id: bigwig_to_bedgraph + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2024-08-02' + Description: Load model from BioImage.IO and make inferences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Machine learning + - Computer science + EDAM topic (no superclasses): + - Machine learning + Galaxy tool ids: + - bioimage_inference + Galaxy wrapper id: bioimaging + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging + Galaxy wrapper version: 2.4.1 + No. of tool users (5 years) (usegalaxy.eu): 2 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2 + No. of tool users (all time) (usegalaxy.eu): 2 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2 + Source: https://github.com/bgruening/galaxytools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Imaging + ToolShed id: bioimage_inference + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: pytorch + bio.tool description: PyTorch is an optimized tensor library for deep learning using + GPUs and CPUs. + bio.tool id: pytorch + bio.tool ids: + - pytorch + bio.tool name: PyTorch +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-11-07' + Description: Wrappers for tools to bring BioModels AI models into Galaxy. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - biomodels_biomd0000001066 + - biomodels_biomd0000001076 + Galaxy wrapper id: biomodelsML + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 25 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 25 + No. of tool users (all time) (usegalaxy.eu): 25 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 25 + Source: https://www.ebi.ac.uk/biomodels/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Machine Learning + ToolShed id: biomodels + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-05-17' + Description: Bionano Solve is a set of tools for analyzing Bionano data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bionano_scaffold + Galaxy wrapper id: bionano + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/bionano + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/bionano + Galaxy wrapper version: 3.7.0 + No. of tool users (5 years) (usegalaxy.eu): 547 + No. of tool users (5 years) (usegalaxy.org): 143 + No. of tool users (5 years) (usegalaxy.org.au): 596 + No. of tool users (5 years) - all main servers: 1286 + No. of tool users (all time) (usegalaxy.eu): 547 + No. of tool users (all time) (usegalaxy.org): 143 + No. of tool users (all time) (usegalaxy.org.au): 596 + No. of tool users (all time) - all main servers: 1286 + Source: https://bionanogenomics.com/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 151 + Tool usage (5 years) (usegalaxy.org): 43 + Tool usage (5 years) (usegalaxy.org.au): 22 + Tool usage (5 years) - all main servers: 216 + Tool usage (all time) (usegalaxy.eu): 151 + Tool usage (all time) (usegalaxy.org): 43 + Tool usage (all time) (usegalaxy.org.au): 22 + Tool usage (all time) - all main servers: 216 + ToolShed categories: + - Assembly + ToolShed id: bionano + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 4 + Conda id: bismark + Conda version: 0.24.2 + Date of first commit of the suite: '2018-08-22' + Description: A tool to map bisulfite converted sequence reads and determine cytosine + methylation states + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bismark_pretty_report + - bismark_bowtie2 + - bismark_deduplicate + - bismark_methylation_extractor + Galaxy wrapper id: bismark + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/bismark + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/bismark + Galaxy wrapper version: 0.22.1 + No. of tool users (5 years) (usegalaxy.eu): 13715 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 197 + No. of tool users (5 years) - all main servers: 13912 + No. of tool users (all time) (usegalaxy.eu): 14997 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 197 + No. of tool users (all time) - all main servers: 15194 + Source: https://www.bioinformatics.babraham.ac.uk/projects/bismark/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 992 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 22 + Tool usage (5 years) - all main servers: 1014 + Tool usage (all time) (usegalaxy.eu): 1099 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 22 + Tool usage (all time) - all main servers: 1121 + ToolShed categories: + - Sequence Analysis + - Next Gen Mappers + ToolShed id: bismark + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 4 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 4 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 4 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 4 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 4 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 4 + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 4 + UseGalaxy.no: 4 + UseGalaxy.or: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-11-10' + Description: Identification and isolation non-target data in draft and publicly + available genome assemblies. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - blobtoolkit + Galaxy wrapper id: blobtoolkit + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit + Galaxy wrapper version: 4.0.7 + No. of tool users (5 years) (usegalaxy.eu): 1527 + No. of tool users (5 years) (usegalaxy.org): 6 + No. of tool users (5 years) (usegalaxy.org.au): 317 + No. of tool users (5 years) - all main servers: 1850 + No. of tool users (all time) (usegalaxy.eu): 1527 + No. of tool users (all time) (usegalaxy.org): 6 + No. of tool users (all time) (usegalaxy.org.au): 317 + No. of tool users (all time) - all main servers: 1850 + Source: https://blobtoolkit.genomehubs.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 79 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 26 + Tool usage (5 years) - all main servers: 106 + Tool usage (all time) (usegalaxy.eu): 79 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 26 + Tool usage (all time) - all main servers: 106 + ToolShed categories: + - Sequence Analysis + - Assembly + ToolShed id: blobtoolkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: blockbuster + Conda version: 0.0.1.1 + Date of first commit of the suite: '2015-02-28' + Description: Blockbuster detects blocks of overlapping reads using a gaussian-distribution + approach. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - blockbuster + Galaxy wrapper id: blockbuster + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 768 + No. of tool users (5 years) (usegalaxy.org): 14 + No. of tool users (5 years) (usegalaxy.org.au): 276 + No. of tool users (5 years) - all main servers: 1058 + No. of tool users (all time) (usegalaxy.eu): 3043 + No. of tool users (all time) (usegalaxy.org): 14 + No. of tool users (all time) (usegalaxy.org.au): 276 + No. of tool users (all time) - all main servers: 3333 + Source: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 97 + Tool usage (5 years) (usegalaxy.org): 11 + Tool usage (5 years) (usegalaxy.org.au): 9 + Tool usage (5 years) - all main servers: 117 + Tool usage (all time) (usegalaxy.eu): 119 + Tool usage (all time) (usegalaxy.org): 11 + Tool usage (all time) (usegalaxy.org.au): 9 + Tool usage (all time) - all main servers: 139 + ToolShed categories: + - RNA + - Sequence Analysis + ToolShed id: blockbuster + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: canu + Conda version: '2.2' + Date of first commit of the suite: '2018-06-07' + Description: Canu is a hierarchical assembly pipeline designed for high-noise single-molecule + sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). + EDAM operation: + - De-novo assembly + EDAM operation (no superclasses): + - De-novo assembly + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - canu + Galaxy wrapper id: canu + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/canu + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/canu + Galaxy wrapper version: '2.2' + No. of tool users (5 years) (usegalaxy.eu): 13360 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 3542 + No. of tool users (5 years) - all main servers: 16902 + No. of tool users (all time) (usegalaxy.eu): 14618 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 3542 + No. of tool users (all time) - all main servers: 18160 + Source: https://github.com/marbl/canu + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1383 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 385 + Tool usage (5 years) - all main servers: 1768 + Tool usage (all time) (usegalaxy.eu): 1444 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 385 + Tool usage (all time) - all main servers: 1829 + ToolShed categories: [] + ToolShed id: canu + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: De-novo assembly tool for long read chemistry like Nanopore + data and PacBio data. + bio.tool id: canu + bio.tool ids: + - canu + bio.tool name: CANU +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cellpose + Conda version: null + Date of first commit of the suite: '2024-02-29' + Description: Cellpose is an anatomical segmentation algorithm + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cellpose + Galaxy wrapper id: cellpose + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/cellpose + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/cellpose + Galaxy wrapper version: 3.0.10 + No. of tool users (5 years) (usegalaxy.eu): 14 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 14 + No. of tool users (all time) (usegalaxy.eu): 14 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 14 + Source: https://github.com/MouseLand/cellpose + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Imaging + ToolShed id: cellpose + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 23 + Available on UseGalaxy.fr: 19 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 23 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-05-05' + Description: cellProfiler wrapper + EDAM operation: + - Quantification + - Image analysis + - Parsing + EDAM operation (no superclasses): + - Quantification + - Image analysis + - Parsing + EDAM topic: + - Imaging + - Microarray experiment + - Genotype and phenotype + EDAM topic (no superclasses): + - Imaging + - Microarray experiment + - Genotype and phenotype + Galaxy tool ids: + - cp_cellprofiler + - cp_color_to_gray + - cp_convert_objects_to_image + - cp_display_data_on_image + - cp_enhance_or_suppress_features + - cp_export_to_spreadsheet + - cp_gray_to_color + - cp_identify_primary_objects + - cp_image_math + - cp_mask_image + - cp_measure_granularity + - cp_measure_image_area_occupied + - cp_measure_image_intensity + - cp_measure_image_quality + - cp_measure_object_intensity + - cp_measure_object_size_shape + - cp_measure_texture + - cp_overlay_outlines + - cp_relate_objects + - cp_save_images + - cp_common + - cp_tile + - cp_track_objects + Galaxy wrapper id: cellprofiler + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 4773 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 5688 + No. of tool users (5 years) - all main servers: 10461 + No. of tool users (all time) (usegalaxy.eu): 4773 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 5688 + No. of tool users (all time) - all main servers: 10461 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 749 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 94 + Tool usage (5 years) - all main servers: 843 + Tool usage (all time) (usegalaxy.eu): 749 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 94 + Tool usage (all time) - all main servers: 843 + ToolShed categories: + - Imaging + ToolShed id: cellprofiler + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 19 + Tools available on UseGalaxy.cz: 23 + Tools available on UseGalaxy.eu: 23 + Tools available on UseGalaxy.fr: 19 + Tools available on UseGalaxy.no: 19 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 23 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 19 + UseGalaxy.cz: 23 + UseGalaxy.eu: 23 + UseGalaxy.fr: 19 + UseGalaxy.no: 19 + UseGalaxy.or: 23 + biii: cellprofiler + bio.tool description: Tool for quantifying data from biological images, particularly + in high-throughput experiments. + bio.tool id: CellProfiler + bio.tool ids: + - CellProfiler + bio.tool name: CellProfiler +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-09-15' + Description: cellProfiler4 wrapper + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cp_cellprofiler4 + Galaxy wrapper id: cellprofiler_v4 + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools + Galaxy wrapper version: 4.2.7 + No. of tool users (5 years) (usegalaxy.eu): 55 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 55 + No. of tool users (all time) (usegalaxy.eu): 55 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 55 + Source: https://github.com/CellProfiler/CellProfiler + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Imaging + ToolShed id: cellprofiler4 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2024-08-12' + Description: Using the OpenAI GPT models to generate text based on user input. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - chatgpt_openai_api + Galaxy wrapper id: chatgpt + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt + Galaxy wrapper version: '2024' + No. of tool users (5 years) (usegalaxy.eu): 62 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 62 + No. of tool users (all time) (usegalaxy.eu): 62 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 62 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt + Status: To update + Tool usage (5 years) (usegalaxy.eu): 12 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 12 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - Machine Learning + ToolShed id: chatgpt_openai_api + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-chipseeker + Conda version: 1.38.0 + Date of first commit of the suite: '2018-05-28' + Description: A tool for ChIP peak annotation and visualization + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - chipseeker + Galaxy wrapper id: chipseeker + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker + Galaxy wrapper version: 1.32.0 + No. of tool users (5 years) (usegalaxy.eu): 16468 + No. of tool users (5 years) (usegalaxy.org): 33692 + No. of tool users (5 years) (usegalaxy.org.au): 2948 + No. of tool users (5 years) - all main servers: 53108 + No. of tool users (all time) (usegalaxy.eu): 18344 + No. of tool users (all time) (usegalaxy.org): 34453 + No. of tool users (all time) (usegalaxy.org.au): 2948 + No. of tool users (all time) - all main servers: 55745 + Source: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 956 + Tool usage (5 years) (usegalaxy.org): 2559 + Tool usage (5 years) (usegalaxy.org.au): 104 + Tool usage (5 years) - all main servers: 3619 + Tool usage (all time) (usegalaxy.eu): 991 + Tool usage (all time) (usegalaxy.org): 2625 + Tool usage (all time) (usegalaxy.org.au): 104 + Tool usage (all time) - all main servers: 3720 + ToolShed categories: + - ChIP-seq + - Genome annotation + ToolShed id: chipseeker + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: circexplorer + Conda version: 1.1.10 + Date of first commit of the suite: '2016-06-06' + Description: A combined strategy to identify circular RNAs (circRNAs and ciRNAs) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - circexplorer + Galaxy wrapper id: circexplorer + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer + Galaxy wrapper version: 1.1.9.0 + No. of tool users (5 years) (usegalaxy.eu): 211 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 209 + No. of tool users (5 years) - all main servers: 420 + No. of tool users (all time) (usegalaxy.eu): 263 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 209 + No. of tool users (all time) - all main servers: 472 + Source: https://github.com/YangLab/CIRCexplorer + Status: To update + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 6 + Tool usage (5 years) - all main servers: 38 + Tool usage (all time) (usegalaxy.eu): 40 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 6 + Tool usage (all time) - all main servers: 46 + ToolShed categories: + - Sequence Analysis + - RNA + ToolShed id: circexplorer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2023-07-20' + Description: Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances + and gene families/pathways abundances + EDAM operation: + - Aggregation + EDAM operation (no superclasses): + - Aggregation + EDAM topic: + - Metagenomics + - Molecular interactions, pathways and networks + EDAM topic (no superclasses): + - Metagenomics + - Molecular interactions, pathways and networks + Galaxy tool ids: + - combine_metaphlan_humann + Galaxy wrapper id: combine_metaphlan_humann + Galaxy wrapper owner: bebatut + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 + Galaxy wrapper version: 0.3.0 + No. of tool users (5 years) (usegalaxy.eu): 530 + No. of tool users (5 years) (usegalaxy.org): 8 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 538 + No. of tool users (all time) (usegalaxy.eu): 530 + No. of tool users (all time) (usegalaxy.org): 8 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 538 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 65 + Tool usage (5 years) (usegalaxy.org): 6 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 71 + Tool usage (all time) (usegalaxy.eu): 65 + Tool usage (all time) (usegalaxy.org): 6 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 71 + ToolShed categories: + - Metagenomics + ToolShed id: combine_metaphlan2_humann2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This tool combine MetaPhlAn outputs and HUMANnN outputs + bio.tool id: combine_metaphlan_and_humann + bio.tool ids: + - combine_metaphlan_and_humann + bio.tool name: Combine Metaphlan and HUMAnN +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-10-19' + Description: Compare outputs of HUMAnN2 for several samples and extract similar + and specific information + EDAM operation: + - Comparison + EDAM operation (no superclasses): + - Comparison + EDAM topic: + - Metagenomics + - Gene and protein families + EDAM topic (no superclasses): + - Metagenomics + - Gene and protein families + Galaxy tool ids: + - compare_humann2_output + Galaxy wrapper id: compare_humann2_output + Galaxy wrapper owner: bebatut + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 306 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - 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compare_humann2_outputs + bio.tool name: Compare HUMAnN2 outputs +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: cpat + Conda version: 3.0.5 + Date of first commit of the suite: '2023-02-01' + Description: Coding-potential assessment tool using an alignment-free logistic regression + model. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cpat + Galaxy wrapper id: cpat + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/cpat + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/cpat + Galaxy wrapper version: 3.0.5 + No. of tool users (5 years) (usegalaxy.eu): 204 + No. of tool users (5 years) (usegalaxy.org): 165 + No. of tool users (5 years) (usegalaxy.org.au): 125 + No. of tool users (5 years) - all main servers: 494 + No. of tool users (all time) (usegalaxy.eu): 204 + No. of tool users (all time) (usegalaxy.org): 165 + No. of tool users (all time) (usegalaxy.org.au): 125 + No. of tool users (all time) - all main servers: 494 + Source: https://github.com/liguowang/cpat + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 47 + Tool usage (5 years) (usegalaxy.org): 40 + Tool usage (5 years) (usegalaxy.org.au): 7 + Tool usage (5 years) - all main servers: 94 + Tool usage (all time) (usegalaxy.eu): 47 + Tool usage (all time) (usegalaxy.org): 40 + Tool usage (all time) (usegalaxy.org.au): 7 + Tool usage (all time) - all main servers: 94 + ToolShed categories: + - Transcriptomics + ToolShed id: cpat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: crisper_recognition_tool + Conda version: '1.2' + Date of first commit of the suite: '2015-02-28' + Description: CRISPR Recognition Tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - crispr_recognition_tool + Galaxy wrapper id: crt + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/crt + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/crt + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 4066 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4066 + No. of tool users (all time) (usegalaxy.eu): 4139 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4139 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 166 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 166 + Tool usage (all time) (usegalaxy.eu): 180 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 180 + ToolShed categories: + - Sequence Analysis + ToolShed id: crispr_recognition_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: diffutils + Conda version: null + Date of first commit of the suite: '2020-03-29' + Description: GNU diff tool that calculates the differences between two files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - diff + Galaxy wrapper id: diff + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/diff + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/diff + Galaxy wrapper version: '3.7' + No. of tool users (5 years) (usegalaxy.eu): 362 + No. of tool users (5 years) (usegalaxy.org): 23 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 385 + No. of tool users (all time) (usegalaxy.eu): 362 + No. of tool users (all time) (usegalaxy.org): 23 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 385 + Source: http://www.gnu.org/software/diffutils/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 99 + Tool usage (5 years) (usegalaxy.org): 17 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 116 + Tool usage (all time) (usegalaxy.eu): 99 + Tool usage (all time) (usegalaxy.org): 17 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 116 + ToolShed categories: + - Text Manipulation + ToolShed id: diff + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Diffbind provides functions for processing ChIP-Seq data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: [] + Galaxy wrapper id: diffbind + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/diffbind + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/diffbind + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://bioconductor.org/packages/release/bioc/html/DiffBind.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - ChIP-seq + ToolShed id: diffbind + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: reportlab + Conda version: null + Date of first commit of the suite: '2024-06-07' + Description: A tool to compile assembly reports and stastics from assembly pipeline + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - make_ear + Galaxy wrapper id: ear + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/ear + Galaxy wrapper source: https://github.com/ERGA-consortium/EARs/tree/main + Galaxy wrapper version: 24.10.15 + No. of tool users (5 years) (usegalaxy.eu): 28 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 28 + No. of tool users (all time) (usegalaxy.eu): 28 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 28 + Source: https://github.com/ERGA-consortium/EARs/tree/main + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Sequence Analysis + - Assembly + ToolShed id: erga_ear + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: edta + Conda version: 2.2.0 + Date of first commit of the suite: '2022-10-16' + Description: 'The EDTA package was designed to filter out false discoveries in raw + TE candidates and generate a high-quality non-redundant TE library for whole-genome + TE annotations. ' + EDAM operation: + - De-novo assembly + - Deisotoping + - Genome annotation + EDAM operation (no superclasses): + - De-novo assembly + - Deisotoping + - Genome annotation + EDAM topic: + - Workflows + - Mobile genetic elements + - Plant biology + - Transcription factors and regulatory sites + - Model organisms + EDAM topic (no superclasses): + - Workflows + - Mobile genetic elements + - Plant biology + - Transcription factors and regulatory sites + - Model organisms + Galaxy tool ids: + - edta + Galaxy wrapper id: edta + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/edta + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 4495 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4495 + No. of tool users (all time) (usegalaxy.eu): 4495 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4495 + Source: https://github.com/oushujun/EDTA + Status: To update + Tool usage (5 years) (usegalaxy.eu): 111 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 111 + Tool usage (all time) (usegalaxy.eu): 111 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 111 + ToolShed categories: + - Variant Analysis + ToolShed id: edta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: The EDTA package was designed to filter out false discoveries + in raw TE candidates and generate a high-quality non-redundant TE library for + whole-genome TE annotations. Selection of initial search programs were based on + benckmarkings on the annotation performance using a manually curated TE library + in the rice genome. + bio.tool id: edta + bio.tool ids: + - edta + bio.tool name: The Extensive de novo TE Annotator (EDTA) +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: epicseg + Conda version: '1.0' + Date of first commit of the suite: '2018-03-02' + Description: EpiCSeg is a tool for conducting chromatin segmentation. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - epicseg_segment + Galaxy wrapper id: epicseg + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/epicseg + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/epicseg + Galaxy wrapper version: '@VERSION_STRING@' + No. of tool users (5 years) (usegalaxy.eu): 160 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 160 + No. of tool users (all time) (usegalaxy.eu): 252 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 252 + Source: https://github.com/lamortenera/epicseg + Status: To update + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 21 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 21 + ToolShed categories: + - Epigenetics + ToolShed id: epicseg + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: fastq_utils + Conda version: 0.25.2 + Date of first commit of the suite: '2021-09-12' + Description: FASTQ info allows to validate single or paired fastq files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_info + Galaxy wrapper id: fastq_info + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info + Galaxy wrapper version: 0.25.1 + No. of tool users (5 years) (usegalaxy.eu): 7560 + No. of tool users (5 years) (usegalaxy.org): 6539 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 14099 + No. of tool users (all time) (usegalaxy.eu): 7560 + No. of tool users (all time) (usegalaxy.org): 6539 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 14099 + Source: https://github.com/nunofonseca/fastq_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1266 + Tool usage (5 years) (usegalaxy.org): 1581 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2847 + Tool usage (all time) (usegalaxy.eu): 1266 + Tool usage (all time) (usegalaxy.org): 1581 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2847 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastq_info + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: This tool returns all unique lines from a tab-separated file. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bg_uniq + Galaxy wrapper id: file_manipulation + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation + Galaxy wrapper version: '0.4' + No. of tool users (5 years) (usegalaxy.eu): 6690 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6690 + No. of tool users (all time) (usegalaxy.eu): 8818 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8818 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation + Status: To update + Tool usage (5 years) (usegalaxy.eu): 554 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 554 + Tool usage (all time) (usegalaxy.eu): 612 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 612 + ToolShed categories: + - Text Manipulation + ToolShed id: unique + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: biopython + Conda version: '1.70' + Date of first commit of the suite: '2015-03-19' + Description: null + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bg_find_subsequences + Galaxy wrapper id: find_subsequences + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences + Galaxy wrapper source: null + Galaxy wrapper version: '0.3' + No. of tool users (5 years) (usegalaxy.eu): 554 + No. of tool users (5 years) (usegalaxy.org): 2820 + No. of tool users (5 years) (usegalaxy.org.au): 20 + No. of tool users (5 years) - all main servers: 3394 + No. of tool users (all time) (usegalaxy.eu): 784 + No. of tool users (all time) (usegalaxy.org): 3047 + No. of tool users (all time) (usegalaxy.org.au): 20 + No. of tool users (all time) - all main servers: 3851 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 69 + Tool usage (5 years) (usegalaxy.org): 323 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 393 + Tool usage (all time) (usegalaxy.eu): 79 + Tool usage (all time) (usegalaxy.org): 361 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 441 + ToolShed categories: [] + ToolShed id: find_subsequences + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: flexynesis + Conda version: 0.2.10 + Date of first commit of the suite: '2024-08-12' + Description: This is a deep-learning based multi-omics bulk sequencing data integration + suite with a focus on (pre-)clinical endpoint prediction. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - flexynesis + Galaxy wrapper id: flexynesis + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis + Galaxy wrapper version: 0.2.10 + No. of tool users (5 years) (usegalaxy.eu): 9 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 9 + No. of tool users (all time) (usegalaxy.eu): 9 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 9 + Source: https://github.com/BIMSBbioinfo/flexynesis/tree/main + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Machine Learning + - Statistics + - Systems Biology + ToolShed id: flexynesis + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2024-10-14' + Description: Using the black forest labs FLUX.1 models to generate image based on + user input. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - black_forest_labs_flux + Galaxy wrapper id: flux + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/flux + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/flux + Galaxy wrapper version: '2024' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/cflux + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Machine Learning + ToolShed id: black_forest_labs_flux + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: flye + Conda version: 2.9.5 + Date of first commit of the suite: '2018-09-24' + Description: Assembly of long and error-prone reads. + EDAM operation: + - Genome assembly + - De-novo assembly + - Mapping assembly + - Cross-assembly + EDAM operation (no superclasses): + - Genome assembly + - De-novo assembly + - Mapping assembly + - Cross-assembly + EDAM topic: + - Sequence assembly + - Metagenomics + - Whole genome sequencing + - Genomics + EDAM topic (no superclasses): + - Sequence assembly + - Metagenomics + - Whole genome sequencing + Galaxy tool ids: + - flye + Galaxy wrapper id: flye + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/flye + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/flye + Galaxy wrapper version: 2.9.5 + No. of tool users (5 years) (usegalaxy.eu): 32514 + No. of tool users (5 years) (usegalaxy.org): 19434 + No. of tool users (5 years) (usegalaxy.org.au): 9843 + No. of tool users (5 years) - all main servers: 61791 + No. of tool users (all time) (usegalaxy.eu): 32675 + No. of tool users (all time) (usegalaxy.org): 19434 + No. of tool users (all time) (usegalaxy.org.au): 9843 + No. of tool users (all time) - all main servers: 61952 + Source: https://github.com/fenderglass/Flye/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 3379 + Tool usage (5 years) (usegalaxy.org): 2537 + Tool usage (5 years) (usegalaxy.org.au): 1624 + Tool usage (5 years) - all main servers: 7540 + Tool usage (all time) (usegalaxy.eu): 3422 + Tool usage (all time) (usegalaxy.org): 2537 + Tool usage (all time) (usegalaxy.org.au): 1624 + Tool usage (all time) - all main servers: 7583 + ToolShed categories: + - Assembly + ToolShed id: flye + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'Flye is a de novo assembler for single molecule sequencing + reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is + designed for a wide range of datasets, from small bacterial projects to large + mammalian-scale assemblies. The package represents a complete pipeline: it takes + raw PB / ONT reads as input and outputs polished contigs.' + bio.tool id: Flye + bio.tool ids: + - Flye + bio.tool name: Flye +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: footprint + Conda version: 1.0.1 + Date of first commit of the suite: '2017-04-18' + Description: Find transcription factor footprints + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - footprint + Galaxy wrapper id: footprint + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/footprint + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/footprint + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 57 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 57 + No. of tool users (all time) (usegalaxy.eu): 57 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 57 + Source: https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Epigenetics + ToolShed id: footprint + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-10-19' + Description: Format CD-hit output to rename representative sequences with cluster + name and/or extract distribution inside clusters given a mapping file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - format_cd_hit_output + Galaxy wrapper id: format_cd_hit_output + Galaxy wrapper owner: bebatut + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ + Galaxy wrapper version: 1.0.0+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 189 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 189 + No. of tool users (all time) (usegalaxy.eu): 203 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 203 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 57 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 57 + Tool usage (all time) (usegalaxy.eu): 60 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 60 + ToolShed categories: + - Fasta Manipulation + ToolShed id: format_cd_hit_output + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-10-19' + Description: Format MetaPhlAn2 output to extract abundance at different taxonomic + levels + EDAM operation: + - Formatting + EDAM operation (no superclasses): + - Formatting + EDAM topic: + - Taxonomy + - Metagenomics + EDAM topic (no superclasses): + - Taxonomy + - Metagenomics + Galaxy tool ids: + - format_metaphlan2_output + Galaxy wrapper id: format_metaphlan2_output + Galaxy wrapper owner: bebatut + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 5940 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5940 + No. of tool users (all time) (usegalaxy.eu): 6474 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6474 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 558 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 558 + Tool usage (all time) (usegalaxy.eu): 608 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 608 + ToolShed categories: + - Metagenomics + ToolShed id: format_metaphlan2_output + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: This tool format output file of MetaPhlan2 containing community + content (abundance) at all taxonomic levels (from kingdom to strains). + bio.tool id: format_metaphlan2_output + bio.tool ids: + - format_metaphlan2_output + bio.tool name: Format metaphlan2 output +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: gfastats + Conda version: 1.3.8 + Date of first commit of the suite: '2022-03-08' + Description: Tool for generating sequence statistics and simultaneous genome assembly + file manipulation. + EDAM operation: + - Data handling + EDAM operation (no superclasses): + - Data handling + EDAM topic: + - Computational biology + EDAM topic (no superclasses): + - Computational biology + Galaxy tool ids: + - gfastats + Galaxy wrapper id: gfastats + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/gfastats + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/gfastats + Galaxy wrapper version: 1.3.8 + No. of tool users (5 years) (usegalaxy.eu): 11748 + No. of tool users (5 years) (usegalaxy.org): 6560 + No. of tool users (5 years) (usegalaxy.org.au): 2556 + No. of tool users (5 years) - 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gfastats + bio.tool name: gfastats +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: GlimmerHMM is a new gene finder based on a Generalized Hidden Markov + Model (GHMM) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: [] + Galaxy wrapper id: glimmer_hmm + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://ccb.jhu.edu/software/glimmerhmm/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: glimmer_hmm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: gotohscan + Conda version: '1.3' + Date of first commit of the suite: '2015-07-02' + Description: Find subsequences in db + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - 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all main servers: 7 + ToolShed categories: + - Sequence Analysis + ToolShed id: gotohscan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Convert between different graph formats + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - 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all main servers: 0 + ToolShed categories: + - Convert Formats + ToolShed id: graph_converter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: GraphClust + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: GraphClust can be used for structural clustering of RNA sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - graphclust + Galaxy wrapper id: graphclust + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/graphclust + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/graphclust + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 6 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6 + Source: http://www.bioinf.uni-freiburg.de/Software/GraphClust/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - RNA + ToolShed id: graphclust + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphmap + Conda version: 0.6.4 + Date of first commit of the suite: '2018-09-27' + Description: Mapper for long, error-prone reads. + EDAM operation: + - Sequence trimming + - EST assembly + - Read mapping + EDAM operation (no superclasses): + - Sequence trimming + - EST assembly + - Read mapping + EDAM topic: + - Gene transcripts + - RNA-Seq + - RNA splicing + EDAM topic (no superclasses): + - Gene transcripts + - RNA-Seq + - RNA splicing + Galaxy tool ids: + - graphmap_align + - graphmap_overlap + Galaxy wrapper id: graphmap + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/graphmap + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/graphmap + Galaxy wrapper version: 0.5.2 + No. of tool users (5 years) (usegalaxy.eu): 7012 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7012 + No. of tool users (all time) (usegalaxy.eu): 7344 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7344 + Source: https://github.com/isovic/graphmap/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 323 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 323 + Tool usage (all time) (usegalaxy.eu): 338 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 338 + ToolShed categories: + - Assembly + ToolShed id: graphmap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + biii: null + bio.tool description: Splice-aware RNA-seq mapper for long reads | GraphMap - A + highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html + https://www.biorxiv.org/content/10.1101/720458v1 + bio.tool id: graphmap + bio.tool ids: + - graphmap + bio.tool name: graphmap +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hclust2 + Conda version: 1.0.0 + Date of first commit of the suite: '2018-07-22' + Description: Plots heatmaps + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hclust2 + Galaxy wrapper id: hclust2 + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 + Galaxy wrapper source: https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 + Galaxy wrapper version: '0.99' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - 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hictk + Galaxy wrapper id: hictk + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/hictk + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/hictk + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 17 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 17 + No. of tool users (all time) (usegalaxy.eu): 17 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 17 + Source: https://github.com/paulsengroup/hictk + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Convert Formats + - Epigenetics + ToolShed id: hictk + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 7 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2017-03-09' + Description: The HiCUP-Pipeline from the Bioinformatics Babraham Institute. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hicup2juicer + - hicup_deduplicator + - hicup_digester + - hicup_filter + - hicup_hicup + - hicup_mapper + - hicup_truncater + Galaxy wrapper id: hicup + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/hicup + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/hicup + Galaxy wrapper version: 0.9.2 + No. of tool users (5 years) (usegalaxy.eu): 901 + No. of tool users (5 years) (usegalaxy.org): 440 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1341 + No. of tool users (all time) (usegalaxy.eu): 1020 + No. of tool users (all time) (usegalaxy.org): 440 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1460 + Source: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 160 + Tool usage (5 years) (usegalaxy.org): 111 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 271 + Tool usage (all time) (usegalaxy.eu): 184 + Tool usage (all time) (usegalaxy.org): 111 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 295 + ToolShed categories: + - Epigenetics + ToolShed id: hicup + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 6 + Tools available on UseGalaxy.org (Main): 7 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + UseGalaxy.no: 6 + UseGalaxy.or: 7 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Software for motif discovery and next generation sequencing analysis. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: [] + Galaxy wrapper id: homer + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/homer + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/homer + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://homer.salk.edu/homer/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: homer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: Rscript + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Methylation analyzer for Illumina 450k DNA emthylation microarrays + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - illumina_methylation_analyser + Galaxy wrapper id: illumina_methylation_analyser + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: illumina_methylation_analyser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: wget + Conda version: null + Date of first commit of the suite: '2023-12-06' + Description: Tool to query ftp links for study from bioimage archive + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bia_download + Galaxy wrapper id: bia-ftplinks + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 3 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3 + No. of tool users (all time) (usegalaxy.eu): 3 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Imaging + ToolShed id: bia_download + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: graphicsmagick + Conda version: 1.3.26 + Date of first commit of the suite: '2016-12-26' + Description: Contains tools based on GraphicsMagick + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - graphicsmagick_image_compare + - graphicsmagick_image_convert + - graphicsmagick_image_montage + Galaxy wrapper id: graphicsmagick + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick + Galaxy wrapper source: https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ + Galaxy wrapper version: 1.3.45 + No. of tool users (5 years) (usegalaxy.eu): 1725 + No. of tool users (5 years) (usegalaxy.org): 2 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1727 + No. of tool users (all time) (usegalaxy.eu): 2708 + No. of tool users (all time) (usegalaxy.org): 2 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2710 + Source: http://www.graphicsmagick.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 97 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 99 + Tool usage (all time) (usegalaxy.eu): 99 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 101 + ToolShed categories: + - Imaging + ToolShed id: graphicsmagick + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 3 + UseGalaxy.no: 2 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 27 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-09-09' + Description: ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage + data, with a focus on scientific imaging. + EDAM operation: + - Image analysis + - Image annotation + - Visualisation + EDAM operation (no superclasses): + - Image analysis + - Image annotation + - Visualisation + EDAM topic: + - Imaging + EDAM topic (no superclasses): + - Imaging + Galaxy tool ids: + - imagej2_adjust_threshold_binary + - imagej2_analyze_particles_binary + - imagej2_analyze_skeleton + - imagej2_binary_to_edm + - imagej2_bunwarpj_adapt_transform + - imagej2_bunwarpj_align + - imagej2_bunwarpj_compare_elastic + - imagej2_bunwarpj_compare_elastic_raw + - imagej2_bunwarpj_compare_raw + - imagej2_bunwarpj_compose_elastic + - imagej2_bunwarpj_compose_raw + - imagej2_bunwarpj_compose_raw_elastic + - imagej2_bunwarpj_convert_to_raw + - imagej2_bunwarpj_elastic_transform + - imagej2_bunwarpj_raw_transform + - imagej2_create_image + - imagej2_crop + - imagej2_enhance_contrast + - imagej2_filter + - imagej2_find_edges + - imagej2_find_maxima + - imagej2_make_binary + - imagej2_math + - imagej2_noise + - imagej2_shadows + - imagej2_sharpen + - imagej2_skeletonize3d + - imagej2_smooth + - imagej2_watershed_binary + Galaxy wrapper id: imagej2 + Galaxy wrapper owner: imgteam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 + Galaxy wrapper version: '20240614' + No. of tool users (5 years) (usegalaxy.eu): 1731 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1731 + No. of tool users (all time) (usegalaxy.eu): 1731 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1731 + Source: http://fiji.sc + Status: To update + Tool usage (5 years) (usegalaxy.eu): 109 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 109 + Tool usage (all time) (usegalaxy.eu): 109 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 109 + ToolShed categories: + - Imaging + ToolShed id: imagej2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 27 + Tools available on UseGalaxy.eu: 27 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 27 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 27 + UseGalaxy.eu: 27 + UseGalaxy.no: 27 + biii: imagej2 + bio.tool description: "It is a public domain Java image processing program, which\ + \ was designed with an open architecture. Custom acquisition, analysis and processing\ + \ plugins can be developed using ImageJ\u2019s built-in editor and a Java compiler.\ + \ User-written plugins make it possible to solve many image processing and analysis\ + \ problems, from three-dimensional live-cell imaging, to radiological image processing,\ + \ multiple imaging system data comparisons to automated hematology systems." + bio.tool id: imagej + bio.tool ids: + - imagej + bio.tool name: ImageJ2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: fiji-morpholibj + Conda version: 1.6.1 + Date of first commit of the suite: '2024-02-29' + Description: Tool to automate quantification of wound healing in high-throughput + microscopy scratch assays + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - woundhealing_scratch_assay + Galaxy wrapper id: woundhealing + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools + Galaxy wrapper version: 1.6.1 + No. of tool users (5 years) (usegalaxy.eu): 31 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 31 + No. of tool users (all time) (usegalaxy.eu): 31 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 31 + Source: https://git.embl.de/grp-cba/wound-healing-htm-screen + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Imaging + ToolShed id: Wound healing scratch assay image analysis + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-11-10' + Description: Large genome reassembly based on Hi-C data + EDAM operation: + - Genome assembly + - Mapping assembly + - Genetic mapping + - Scaffolding + EDAM operation (no superclasses): + - Genome assembly + - Mapping assembly + - Genetic mapping + - Scaffolding + EDAM topic: + - Sequence assembly + - Mapping + - Metagenomics + - Statistics and probability + - DNA binding sites + EDAM topic (no superclasses): + - Sequence assembly + - Mapping + - Metagenomics + - Statistics and probability + - DNA binding sites + Galaxy tool ids: + - instagraal + Galaxy wrapper id: instagraal + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/instagraal + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/instagraal + Galaxy wrapper version: 0.1.6 + No. of tool users (5 years) (usegalaxy.eu): 157 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 157 + No. of tool users (all time) (usegalaxy.eu): 157 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 157 + Source: https://github.com/koszullab/instaGRAAL + Status: To update + Tool usage (5 years) (usegalaxy.eu): 14 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 14 + Tool usage (all time) (usegalaxy.eu): 14 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 14 + ToolShed categories: + - Assembly + ToolShed id: instagraal + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: 'Chromosome-level quality scaffolding of brown algal genomes + using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large + genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) + and post-scaffolding polishing libraries.This work is under continuous development/improvement + - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note + to OS X users: There is currently no CUDA support on Mojave (10.14) and it is + unclear when it is going to be added, if it is to be added at all. This means + instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If + you wish to run it on OS X, the only solution for now is to downgrade to High + Sierra (10.13)' + bio.tool id: instagraal + bio.tool ids: + - instagraal + bio.tool name: instaGRAAL +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Interproscan queries the interpro database and provides annotations. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: [] + Galaxy wrapper id: iprscan5 + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://www.ebi.ac.uk/Tools/pfa/iprscan5/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: iprscan5 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: itsx + Conda version: 1.1.3 + Date of first commit of the suite: '2022-05-02' + Description: ITSx is an open source software utility to extract the highly variable + ITS1 and ITS2 subregions from ITS sequences. + EDAM operation: + - Sequence feature detection + EDAM operation (no superclasses): + - Sequence feature detection + EDAM topic: + - Functional, regulatory and non-coding RNA + - Microbiology + EDAM topic (no superclasses): + - Functional, regulatory and non-coding RNA + - Microbiology + Galaxy tool ids: + - itsx + Galaxy wrapper id: itsx + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/itsx + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/itsx + Galaxy wrapper version: 1.1.3 + No. of tool users (5 years) (usegalaxy.eu): 1426 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1426 + No. of tool users (all time) (usegalaxy.eu): 1426 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1426 + Source: https://microbiology.se/software/itsx/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 71 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 71 + Tool usage (all time) (usegalaxy.eu): 71 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 71 + ToolShed categories: + - Metagenomics + ToolShed id: itsx + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: TSx is an open source software utility to extract the highly + variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as + a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, + very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence + identification process can lead to severely misleading results, ITSx identifies + and extracts only the ITS regions themselves. + bio.tool id: ITSx + bio.tool ids: + - ITSx + bio.tool name: ITSx +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: jbrowse2 + Conda version: 2.15.4 + Date of first commit of the suite: '2024-06-04' + Description: JBrowse2 Genome Browser integrated as a Galaxy Tool + EDAM operation: + - Genome visualisation + - Structure visualisation + - Pathway visualisation + EDAM operation (no superclasses): + - Genome visualisation + - Structure visualisation + - Pathway visualisation + EDAM topic: + - Mapping + - Structural variation + - Genomics + - Gene structure + - Sequence assembly + EDAM topic (no superclasses): + - Mapping + - Structural variation + - Genomics + - Gene structure + - Sequence assembly + Galaxy tool ids: + - jbrowse2 + Galaxy wrapper id: jbrowse2 + Galaxy wrapper owner: fubar + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 + Galaxy wrapper version: 2.15.4 + No. of tool users (5 years) (usegalaxy.eu): 1312 + No. of tool users (5 years) (usegalaxy.org): 116 + No. of tool users (5 years) (usegalaxy.org.au): 37 + No. of tool users (5 years) - all main servers: 1465 + No. of tool users (all time) (usegalaxy.eu): 1312 + No. of tool users (all time) (usegalaxy.org): 116 + No. of tool users (all time) (usegalaxy.org.au): 37 + No. of tool users (all time) - all main servers: 1465 + Source: https://jbrowse.org + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 219 + Tool usage (5 years) (usegalaxy.org): 58 + Tool usage (5 years) (usegalaxy.org.au): 6 + Tool usage (5 years) - all main servers: 283 + Tool usage (all time) (usegalaxy.eu): 219 + Tool usage (all time) (usegalaxy.org): 58 + Tool usage (all time) (usegalaxy.org.au): 6 + Tool usage (all time) - all main servers: 283 + ToolShed categories: + - Sequence Analysis + ToolShed id: jbrowse2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Modular genome browser with views of synteny and structural + variation. + bio.tool id: jbrowse_2 + bio.tool ids: + - jbrowse_2 + bio.tool name: JBrowse 2 +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-12-11' + Description: Run jupyter notebook script in Galaxy + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - run_jupyter_job + Galaxy wrapper id: jupyter_job + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 30 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 30 + No. of tool users (all time) (usegalaxy.eu): 30 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 30 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Machine Learning + ToolShed id: run_jupyter_job + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: labels + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: remaps and annotates alignments + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bg_labels + Galaxy wrapper id: labels + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/labels + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/labels + Galaxy wrapper version: 1.0.5.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/labels + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: labels + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: lighter + Conda version: 1.1.3 + Date of first commit of the suite: '2016-06-04' + Description: Lighter is a kmer-based error correction method for whole genome sequencing + data + EDAM operation: + - k-mer counting + - Sequence read processing + - Sequencing quality control + - Sequencing error detection + EDAM operation (no superclasses): + - k-mer counting + - Sequence read processing + - Sequencing quality control + - Sequencing error detection + EDAM topic: + - Sequencing + - Whole genome sequencing + - DNA + - Genomics + EDAM topic (no superclasses): + - Whole genome sequencing + - DNA + - Genomics + Galaxy tool ids: + - lighter + Galaxy wrapper id: lighter + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/lighter + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/lighter + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 149 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 149 + No. of tool users (all time) (usegalaxy.eu): 171 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 171 + Source: https://github.com/mourisl/Lighter + Status: To update + Tool usage (5 years) (usegalaxy.eu): 27 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 27 + Tool usage (all time) (usegalaxy.eu): 30 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 30 + ToolShed categories: + - Sequence Analysis + - Fasta Manipulation + ToolShed id: lighter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Kmer-based error correction method for whole genome sequencing + data. Lighter uses sampling (rather than counting) to obtain a set of kmers that + are likely from the genome. Using this information, Lighter can correct the reads + containing sequence errors. + bio.tool id: lighter + bio.tool ids: + - lighter + bio.tool name: Lighter +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: mafft + Conda version: '7.525' + Date of first commit of the suite: '2023-11-06' + Description: Multiple alignment program for amino acid or nucleotide sequences + EDAM operation: + - Multiple sequence alignment + EDAM operation (no superclasses): + - Multiple sequence alignment + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - rbc_mafft_add + - rbc_mafft + Galaxy wrapper id: mafft + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/mafft + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/mafft + Galaxy wrapper version: '7.526' + No. of tool users (5 years) (usegalaxy.eu): 172433 + No. of tool users (5 years) (usegalaxy.org): 108640 + No. of tool users (5 years) (usegalaxy.org.au): 20027 + No. of tool users (5 years) - all main servers: 301100 + No. of tool users (all time) (usegalaxy.eu): 174456 + No. of tool users (all time) (usegalaxy.org): 122790 + No. of tool users (all time) (usegalaxy.org.au): 20027 + No. of tool users (all time) - all main servers: 317273 + Source: https://mafft.cbrc.jp/alignment/software/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1865 + Tool usage (5 years) (usegalaxy.org): 4266 + Tool usage (5 years) (usegalaxy.org.au): 1172 + Tool usage (5 years) - all main servers: 7303 + Tool usage (all time) (usegalaxy.eu): 1951 + Tool usage (all time) (usegalaxy.org): 5521 + Tool usage (all time) (usegalaxy.org.au): 1172 + Tool usage (all time) - all main servers: 8644 + ToolShed categories: + - RNA + ToolShed id: mafft + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: MAFFT (Multiple Alignment using Fast Fourier Transform) is + a high speed multiple sequence alignment program. + bio.tool id: MAFFT + bio.tool ids: + - MAFFT + bio.tool name: MAFFT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-12-13' + Description: data source for MaveDB + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mavedb_importer + Galaxy wrapper id: mavedb + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ + Galaxy wrapper version: '0.9' + No. of tool users (5 years) (usegalaxy.eu): 8 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 8 + No. of tool users (all time) (usegalaxy.eu): 8 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Data Source + ToolShed id: mavedb_importer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: methtools + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: tools for methylation analysis + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - methtools_calling + - r_correlation_matrix + - methtools_destrand + - methtools_dmr + - methtools_filter + - methtools_plot + - smooth_running_window + - methtools_tiling + Galaxy wrapper id: methtools + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/methtools + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/methtools + Galaxy wrapper version: 0.1.1 + No. of tool users (5 years) (usegalaxy.eu): 632 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 632 + No. of tool users (all time) (usegalaxy.eu): 5461 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5461 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/methtools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 155 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 155 + Tool usage (all time) (usegalaxy.eu): 453 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 453 + ToolShed categories: + - Sequence Analysis + ToolShed id: methtools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: methyldackel + Conda version: 0.6.1 + Date of first commit of the suite: '2017-02-14' + Description: A tool for processing bisulfite sequencing alignments + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pileometh + Galaxy wrapper id: methyldackel + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel + Galaxy wrapper version: 0.5.2 + No. of tool users (5 years) (usegalaxy.eu): 14907 + No. of tool users (5 years) (usegalaxy.org): 2677 + No. of tool users (5 years) (usegalaxy.org.au): 2313 + No. of tool users (5 years) - all main servers: 19897 + No. of tool users (all time) (usegalaxy.eu): 18971 + No. of tool users (all time) (usegalaxy.org): 2677 + No. of tool users (all time) (usegalaxy.org.au): 2313 + No. of tool users (all time) - all main servers: 23961 + Source: https://github.com/dpryan79/MethylDackel + Status: To update + Tool usage (5 years) (usegalaxy.eu): 638 + Tool usage (5 years) (usegalaxy.org): 230 + Tool usage (5 years) (usegalaxy.org.au): 83 + Tool usage (5 years) - all main servers: 951 + Tool usage (all time) (usegalaxy.eu): 894 + Tool usage (all time) (usegalaxy.org): 230 + Tool usage (all time) (usegalaxy.org.au): 83 + Tool usage (all time) - all main servers: 1207 + ToolShed categories: + - Sequence Analysis + ToolShed id: pileometh + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-methylkit + Conda version: 1.28.0 + Date of first commit of the suite: '2016-12-20' + Description: A method for DNA methylation analysis and annotation from high-throughput + bisulfite sequencing. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - methylkit + Galaxy wrapper id: methylkit + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/methylkit + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/methylkit + Galaxy wrapper version: 0.99.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://bioconductor.org/packages/release/bioc/html/methylKit.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Epigenetics + ToolShed id: methylkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: metilene + Conda version: 0.2.8 + Date of first commit of the suite: '2015-12-14' + Description: Differential DNA methylation calling + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - metilene + Galaxy wrapper id: metilene + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/metilene + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/metilene + Galaxy wrapper version: 0.2.6.1 + No. of tool users (5 years) (usegalaxy.eu): 3209 + No. of tool users (5 years) (usegalaxy.org): 479 + No. of tool users (5 years) (usegalaxy.org.au): 315 + No. of tool users (5 years) - all main servers: 4003 + No. of tool users (all time) (usegalaxy.eu): 4572 + No. of tool users (all time) (usegalaxy.org): 479 + No. of tool users (all time) (usegalaxy.org.au): 315 + No. of tool users (all time) - all main servers: 5366 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 312 + Tool usage (5 years) (usegalaxy.org): 79 + Tool usage (5 years) (usegalaxy.org.au): 51 + Tool usage (5 years) - all main servers: 442 + Tool usage (all time) (usegalaxy.eu): 442 + Tool usage (all time) (usegalaxy.org): 79 + Tool usage (all time) (usegalaxy.org.au): 51 + Tool usage (all time) - all main servers: 572 + ToolShed categories: + - RNA + - Statistics + ToolShed id: metilene + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-05-14' + Description: A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. + EDAM operation: + - Nucleic acid design + EDAM operation (no superclasses): + - Nucleic acid design + EDAM topic: + - Genomics + - Sequence assembly + - Sequencing + - Probes and primers + EDAM topic (no superclasses): + - Genomics + - Sequence assembly + - Sequencing + - Probes and primers + Galaxy tool ids: + - mgnify_seqprep + Galaxy wrapper id: mgnify_seqprep + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep + Galaxy wrapper version: '1.2' + No. of tool users (5 years) (usegalaxy.eu): 573 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 573 + No. of tool users (all time) (usegalaxy.eu): 573 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 573 + Source: https://github.com/jstjohn/SeqPrep + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 3 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Fastq Manipulation + - Sequence Analysis + ToolShed id: mgnify_seqprep + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: Strips adapters and optionally merges overlapping paired-end + (or paired-end contamination in mate-pair libraries) illumina style reads. + bio.tool id: seqprep + bio.tool ids: + - seqprep + bio.tool name: SeqPrep +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: Rscript + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Identification of binding sites in CLIP-Seq data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mi_clip + Galaxy wrapper id: miclip + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/miclip + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/miclip + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://cran.r-project.org/src/contrib/Archive/MiClip/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: miclip + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: minced + Conda version: 0.4.2 + Date of first commit of the suite: '2015-02-28' + Description: MinCED - Mining CRISPRs in Environmental Datasets + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - minced + Galaxy wrapper id: minced + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/minced + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/minced + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 1213 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1213 + No. of tool users (all time) (usegalaxy.eu): 1309 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1309 + Source: http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README + Status: To update + Tool usage (5 years) (usegalaxy.eu): 115 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 115 + Tool usage (all time) (usegalaxy.eu): 124 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 124 + ToolShed categories: + - Sequence Analysis + ToolShed id: minced + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: minipolish + Conda version: 0.1.3 + Date of first commit of the suite: '2022-10-19' + Description: Polishing miniasm assemblies + EDAM operation: + - Localised reassembly + - Read depth analysis + EDAM operation (no superclasses): + - Localised reassembly + - Read depth analysis + EDAM topic: + - Sequence assembly + - Sequencing + EDAM topic (no superclasses): + - Sequence assembly + - Sequencing + Galaxy tool ids: + - minipolish + Galaxy wrapper id: minipolish + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/minipolish + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/minipolish + Galaxy wrapper version: 0.1.3 + No. of tool users (5 years) (usegalaxy.eu): 229 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 229 + No. of tool users (all time) (usegalaxy.eu): 229 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 229 + Source: https://github.com/rrwick/Minipolish + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 32 + Tool usage (all time) (usegalaxy.eu): 32 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 32 + ToolShed categories: + - Sequence Analysis + ToolShed id: minipolish + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: A tool that bridges the output of miniasm (long-read assembly) + and racon (assembly polishing) together to polish a draft assembly. It also provides + read depth information in contigs. + bio.tool id: minipolish + bio.tool ids: + - minipolish + bio.tool name: minipolish +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-05-29' + Description: Assembly mitogenomes from Pacbio HiFi read. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mitohifi + Galaxy wrapper id: mitohifi + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi + Galaxy wrapper version: '3' + No. of tool users (5 years) (usegalaxy.eu): 1020 + No. of tool users (5 years) (usegalaxy.org): 414 + No. of tool users (5 years) (usegalaxy.org.au): 277 + No. of tool users (5 years) - all main servers: 1711 + No. of tool users (all time) (usegalaxy.eu): 1020 + No. of tool users (all time) (usegalaxy.org): 414 + No. of tool users (all time) (usegalaxy.org.au): 277 + No. of tool users (all time) - all main servers: 1711 + Source: https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 176 + Tool usage (5 years) (usegalaxy.org): 73 + Tool usage (5 years) (usegalaxy.org.au): 20 + Tool usage (5 years) - all main servers: 269 + Tool usage (all time) (usegalaxy.eu): 176 + Tool usage (all time) (usegalaxy.org): 73 + Tool usage (all time) (usegalaxy.org.au): 20 + Tool usage (all time) - all main servers: 269 + ToolShed categories: + - Assembly + ToolShed id: mitohifi + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: openbabel + Conda version: 2.3.90dev7d621d9 + Date of first commit of the suite: '2015-02-28' + Description: converter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bg_mol2gspan + Galaxy wrapper id: molecule2gspan + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan + Galaxy wrapper version: '0.2' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Convert Formats + ToolShed id: molecule_to_gspan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: motus + Conda version: 3.1.0 + Date of first commit of the suite: '2024-09-06' + Description: Tool for profiling the abundance of microbial taxa. + EDAM operation: + - Taxonomic classification + EDAM operation (no superclasses): + - Taxonomic classification + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - mereg_mOTUs_tables + - motus_profiler + Galaxy wrapper id: motus + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/motus + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs + Galaxy wrapper version: 3.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/motu-tool/mOTUs + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: motus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + biii: null + bio.tool description: Metagenomic operational taxonomic units (mOTUs) enable high-accuracy + taxonomic profiling of known (sequenced) and unknown microorganisms at species-level + resolution from shotgun metagenomic or metatranscriptomic data. The method clusters + single-copy phylogenetic marker gene sequences from metagenomes and reference + genomes into mOTUs to quantify their abundances in meta-omics data with very high + precision and recall. + bio.tool id: mOTUs + bio.tool ids: + - mOTUs + bio.tool name: Metagenomic operational taxonomic units (mOTUs) +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: music-deconvolution + Conda version: 0.1.1 + Date of first commit of the suite: '2021-09-12' + Description: Multi-subject Single Cell deconvolution (MuSiC) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - music_construct_eset + - music_inspect_eset + - music_manipulate_eset + - music_compare + - music_deconvolution + Galaxy wrapper id: music_deconvolution + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ + Galaxy wrapper version: 0.1.1 + No. of tool users (5 years) (usegalaxy.eu): 2801 + No. of tool users (5 years) (usegalaxy.org): 364 + No. of tool users (5 years) (usegalaxy.org.au): 1357 + No. of tool users (5 years) - all main servers: 4522 + No. of tool users (all time) (usegalaxy.eu): 2801 + No. of tool users (all time) (usegalaxy.org): 364 + No. of tool users (all time) (usegalaxy.org.au): 1357 + No. of tool users (all time) - all main servers: 4522 + Source: https://github.com/xuranw/MuSiC + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 289 + Tool usage (5 years) (usegalaxy.org): 80 + Tool usage (5 years) (usegalaxy.org.au): 21 + Tool usage (5 years) - all main servers: 390 + Tool usage (all time) (usegalaxy.eu): 289 + Tool usage (all time) (usegalaxy.org): 80 + Tool usage (all time) (usegalaxy.org.au): 21 + Tool usage (all time) - all main servers: 390 + ToolShed categories: + - Transcriptomics + ToolShed id: music + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 4 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 4 + Conda id: nanopolish + Conda version: 0.14.0 + Date of first commit of the suite: '2018-06-05' + Description: Nanopolish software package for signal-level analysis of Oxford Nanopore + sequencing data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - nanopolish_eventalign + - nanopolish_methylation + - nanopolish_polya + - nanopolish_variants + Galaxy wrapper id: nanopolish + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish + Galaxy wrapper version: 0.14.0 + No. of tool users (5 years) (usegalaxy.eu): 9284 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 2358 + No. of tool users (5 years) - all main servers: 11642 + No. of tool users (all time) (usegalaxy.eu): 9694 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 2358 + No. of tool users (all time) - all main servers: 12052 + Source: https://github.com/jts/nanopolish + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 215 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 49 + Tool usage (5 years) - 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netboxr + Galaxy wrapper id: netboxr + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/netboxr + Galaxy wrapper source: null + Galaxy wrapper version: 1.6.0 + No. of tool users (5 years) (usegalaxy.eu): 12 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 12 + No. of tool users (all time) (usegalaxy.eu): 12 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 12 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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It uses a "correct-then-assemble" strategy similar + to canu (no correction step for PacBio Hifi reads), but requires significantly + less computing resources and storages. + bio.tool id: nextdenovo + bio.tool ids: + - nextdenovo + bio.tool name: NextDenovo +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: nucleosome_prediction + Conda version: '3.0' + Date of first commit of the suite: '2016-09-27' + Description: Prediction of Nucleosomes Positions on the Genome + EDAM operation: + - Prediction and recognition + - Nucleosome position prediction + - Sequence analysis + EDAM operation (no superclasses): + - Prediction and recognition + - Nucleosome position prediction + - Sequence analysis + EDAM topic: + - Structural genomics + - Nucleic acid sites, features and motifs + EDAM topic (no superclasses): + - Structural genomics + - Nucleic acid sites, features and motifs + Galaxy tool ids: + - 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AccurateMassSearch + - AdditiveSeries + - BaselineFilter + - CVInspector + - CompNovo + - CompNovoCID + - ConsensusID + - ConsensusMapNormalizer + - ConvertTSVToTraML + - ConvertTraMLToTSV + - DTAExtractor + - DeMeanderize + - Decharger + - DecoyDatabase + - Digestor + - DigestorMotif + - EICExtractor + - ERPairFinder + - ExternalCalibration + - FFEval + - FalseDiscoveryRate + - FeatureFinderCentroided + - FeatureFinderIdentification + - FeatureFinderIsotopeWavelet + - FeatureFinderMRM + - FeatureFinderMetabo + - FeatureFinderMultiplex + - FeatureFinderSuperHirn + - FeatureLinkerLabeled + - FeatureLinkerUnlabeled + - FeatureLinkerUnlabeledQT + - FidoAdapter + - FileConverter + - FileFilter + - FileInfo + - FileMerger + - FuzzyDiff + - HighResPrecursorMassCorrector + - IDConflictResolver + - IDDecoyProbability + - IDExtractor + - IDFileConverter + - IDFilter + - IDMapper + - IDMassAccuracy + - IDMerger + - IDPosteriorErrorProbability + - IDRTCalibration + - IDRipper + - IDScoreSwitcher + - 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PeakPickerHiRes + - PeakPickerIterative + - PeakPickerWavelet + - PepNovoAdapter + - PeptideIndexer + - PhosphoScoring + - PrecursorIonSelector + - PrecursorMassCorrector + - ProteinInference + - ProteinQuantifier + - ProteinResolver + - QCCalculator + - QCEmbedder + - QCExporter + - QCExtractor + - QCImporter + - QCMerger + - QCShrinker + - RNPxl + - RNPxlXICFilter + - RTEvaluation + - RTModel + - RTPredict + - SemanticValidator + - SequenceCoverageCalculator + - SimpleSearchEngine + - SpecLibCreator + - SpectraFilterBernNorm + - SpectraFilterMarkerMower + - SpectraFilterNLargest + - SpectraFilterNormalizer + - SpectraFilterParentPeakMower + - SpectraFilterScaler + - SpectraFilterSqrtMower + - SpectraFilterThresholdMower + - SpectraFilterWindowMower + - SpectraMerger + - SvmTheoreticalSpectrumGeneratorTrainer + - TICCalculator + - TMTAnalyzer + - TOFCalibration + - TextExporter + - TopPerc + - TransformationEvaluation + - XMLValidator + - XTandemAdapter + Galaxy wrapper id: openms + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/openms + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/openms + Galaxy wrapper version: 2.1.0 + No. of tool users (5 years) (usegalaxy.eu): 31121 + No. of tool users (5 years) (usegalaxy.org): 50 + No. of tool users (5 years) (usegalaxy.org.au): 933 + No. of tool users (5 years) - 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all main servers: 196 + ToolShed categories: + - Sequence Analysis + - RNA + ToolShed id: peakachu + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perf + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: suitable for boolean classification problems + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - stats_perf_tool + Galaxy wrapper id: perf + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/perf + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/perf + Galaxy wrapper version: 5.11.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://osmot.cs.cornell.edu/kddcup/software.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: [] + ToolShed id: stats_perf_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pfam_scan + Conda version: '1.6' + Date of first commit of the suite: '2023-02-02' + Description: Search a FASTA sequence against a library of Pfam HMM. + EDAM operation: + - Protein sequence analysis + EDAM operation (no superclasses): + - Protein sequence analysis + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - pfamscan + Galaxy wrapper id: pfamscan + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan + Galaxy wrapper version: '1.6' + No. of tool users (5 years) (usegalaxy.eu): 773 + No. of tool users (5 years) (usegalaxy.org): 495 + No. of tool users (5 years) (usegalaxy.org.au): 246 + No. of tool users (5 years) - all main servers: 1514 + No. of tool users (all time) (usegalaxy.eu): 773 + No. of tool users (all time) (usegalaxy.org): 495 + No. of tool users (all time) (usegalaxy.org.au): 246 + No. of tool users (all time) - all main servers: 1514 + Source: http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 60 + Tool usage (5 years) (usegalaxy.org): 72 + Tool usage (5 years) (usegalaxy.org.au): 17 + Tool usage (5 years) - 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pfamscan + bio.tool name: PfamScan +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: postgresql + Conda version: null + Date of first commit of the suite: '2017-09-28' + Description: tool suite for dealing with Postgresql databases from Galaxy's history + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pg_dump + - pg_import + - pg_query + Galaxy wrapper id: pg_tools + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tools/pgtools + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://www.postgresql.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Data Export + - Data Source + ToolShed id: pgtools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-01-28' + Description: Pharmacogenomics Clinical Annotation Tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pharmcat + Galaxy wrapper id: pharmcat + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 109 + No. of tool users (5 years) (usegalaxy.org): 250 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 359 + No. of tool users (all time) (usegalaxy.eu): 109 + No. of tool users (all time) (usegalaxy.org): 250 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 359 + Source: https://pharmcat.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 29 + Tool usage (5 years) (usegalaxy.org): 84 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 113 + Tool usage (all time) (usegalaxy.eu): 29 + Tool usage (all time) (usegalaxy.org): 84 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 113 + ToolShed categories: + - Variant Analysis + ToolShed id: pharmcat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: piranha + Conda version: 1.2.1 + Date of first commit of the suite: '2015-07-02' + Description: Piranha is a peak-caller for CLIP- and RIP-Seq data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - piranha + Galaxy wrapper id: piranha + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/piranha + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha + Galaxy wrapper version: 1.2.1.0 + No. of tool users (5 years) (usegalaxy.eu): 1408 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1408 + No. of tool users (all time) (usegalaxy.eu): 2068 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2068 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 94 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 94 + Tool usage (all time) (usegalaxy.eu): 119 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 119 + ToolShed categories: + - Sequence Analysis + - RNA + ToolShed id: piranha + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: platypus + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: efficient and accurate variant-detection in high-throughput sequencing + data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bg_platypus + Galaxy wrapper id: platypus + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/platypus + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/platypus + Galaxy wrapper version: 0.0.11 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://www.well.ox.ac.uk/platypus + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: platypus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy-ml + Conda version: 0.10.0 + Date of first commit of the suite: '2018-10-11' + Description: performance plots for machine learning problems + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - plotly_ml_performance_plots + Galaxy wrapper id: plotly_ml_performance_plots + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots + Galaxy wrapper version: '0.4' + No. of tool users (5 years) (usegalaxy.eu): 1342 + No. of tool users (5 years) (usegalaxy.org): 902 + No. of tool users (5 years) (usegalaxy.org.au): 630 + No. of tool users (5 years) - all main servers: 2874 + No. of tool users (all time) (usegalaxy.eu): 1472 + No. of tool users (all time) (usegalaxy.org): 902 + No. of tool users (all time) (usegalaxy.org.au): 630 + No. of tool users (all time) - all main servers: 3004 + Source: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics + Status: To update + Tool usage (5 years) (usegalaxy.eu): 184 + Tool usage (5 years) (usegalaxy.org): 156 + Tool usage (5 years) (usegalaxy.org.au): 24 + Tool usage (5 years) - 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plotly_parallel_coordinates_plot + Galaxy wrapper id: plotly_parallel_coordinates_plot + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot + Galaxy wrapper version: '0.2' + No. of tool users (5 years) (usegalaxy.eu): 408 + No. of tool users (5 years) (usegalaxy.org): 627 + No. of tool users (5 years) (usegalaxy.org.au): 605 + No. of tool users (5 years) - all main servers: 1640 + No. of tool users (all time) (usegalaxy.eu): 664 + No. of tool users (all time) (usegalaxy.org): 627 + No. of tool users (all time) (usegalaxy.org.au): 605 + No. of tool users (all time) - all main servers: 1896 + Source: https://plot.ly/python/parallel-coordinates-plot/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 91 + Tool usage (5 years) (usegalaxy.org): 118 + Tool usage (5 years) (usegalaxy.org.au): 26 + Tool usage (5 years) - 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plotly_regression_performance_plots + Galaxy wrapper id: plotly_regression_performance_plots + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 764 + No. of tool users (5 years) (usegalaxy.org): 304 + No. of tool users (5 years) (usegalaxy.org.au): 193 + No. of tool users (5 years) - all main servers: 1261 + No. of tool users (all time) (usegalaxy.eu): 879 + No. of tool users (all time) (usegalaxy.org): 304 + No. of tool users (all time) (usegalaxy.org.au): 193 + No. of tool users (all time) - all main servers: 1376 + Source: http://scikit-learn.org/stable/supervised_learning.html#supervised-learning + Status: To update + Tool usage (5 years) (usegalaxy.eu): 213 + Tool usage (5 years) (usegalaxy.org): 95 + Tool usage (5 years) (usegalaxy.org.au): 26 + Tool usage (5 years) - 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eden_protease_prediction + Galaxy wrapper id: protease_prediction + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction + Galaxy wrapper version: '0.9' + No. of tool users (5 years) (usegalaxy.eu): 129 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 129 + No. of tool users (all time) (usegalaxy.eu): 155 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 155 + Source: https://github.com/fabriziocosta/eden + Status: To update + Tool usage (5 years) (usegalaxy.eu): 15 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 15 + Tool usage (all time) (usegalaxy.eu): 21 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 21 + ToolShed categories: + - Sequence Analysis + - Proteomics + ToolShed id: protease_prediction + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: biopython + Conda version: '1.70' + Date of first commit of the suite: '2015-06-07' + Description: Calculation of various properties from given protein sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bg_protein_properties + Galaxy wrapper id: protein_properties + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 465 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 465 + No. of tool users (all time) (usegalaxy.eu): 638 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 638 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 81 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 81 + Tool usage (all time) (usegalaxy.eu): 100 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 100 + ToolShed categories: + - Sequence Analysis + ToolShed id: protein_properties + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Visualisation of PepXML files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomics_improviser + Galaxy wrapper id: improviser + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser + Galaxy wrapper version: 1.1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://www.improviser.uni-freiburg.de/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Proteomics + ToolShed id: proteomics_improviser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: racon + Conda version: 1.5.0 + Date of first commit of the suite: '2018-06-11' + Description: Consensus module for raw de novo DNA assembly of long uncorrected reads. + EDAM operation: + - Genome assembly + - Mapping assembly + EDAM operation (no superclasses): + - Genome assembly + - Mapping assembly + EDAM topic: + - Whole genome sequencing + - Sequence assembly + EDAM topic (no superclasses): + - Whole genome sequencing + - Sequence assembly + Galaxy tool ids: + - racon + Galaxy wrapper id: racon + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/racon + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/racon + Galaxy wrapper version: 1.5.0 + No. of tool users (5 years) (usegalaxy.eu): 27113 + No. of tool users (5 years) (usegalaxy.org): 9089 + No. of tool users (5 years) (usegalaxy.org.au): 5452 + No. of tool users (5 years) - all main servers: 41654 + No. of tool users (all time) (usegalaxy.eu): 27315 + No. of tool users (all time) (usegalaxy.org): 9089 + No. of tool users (all time) (usegalaxy.org.au): 5452 + No. of tool users (all time) - all main servers: 41856 + Source: https://github.com/isovic/racon + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 839 + Tool usage (5 years) (usegalaxy.org): 475 + Tool usage (5 years) (usegalaxy.org.au): 171 + Tool usage (5 years) - all main servers: 1485 + Tool usage (all time) (usegalaxy.eu): 850 + Tool usage (all time) (usegalaxy.org): 475 + Tool usage (all time) (usegalaxy.org.au): 171 + Tool usage (all time) - all main servers: 1496 + ToolShed categories: + - Sequence Analysis + ToolShed id: racon + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Consensus module for raw de novo DNA assembly of long uncorrected + readsRacon is intended as a standalone consensus module to correct raw contigs + generated by rapid assembly methods which do not include a consensus step. The + goal of Racon is to generate genomic consensus which is of similar or better quality + compared to the output generated by assembly methods which employ both error correction + and consensus steps, while providing a speedup of several times compared to those + methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore + Technologies. + bio.tool id: Racon + bio.tool ids: + - Racon + bio.tool name: Racon +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: RepeatMasker + Conda version: 4.0.9_p2 + Date of first commit of the suite: '2015-02-28' + Description: RepeatMasker is a program that screens DNA sequences for interspersed + repeats and low complexity DNA sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - repeatmasker_wrapper + Galaxy wrapper id: repeat_masker + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 5998 + No. of tool users (5 years) (usegalaxy.org): 7618 + No. of tool users (5 years) (usegalaxy.org.au): 3135 + No. of tool users (5 years) - 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replace_column_with_key_value_file + Galaxy wrapper id: replaceColumn + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn + Galaxy wrapper version: '0.2' + No. of tool users (5 years) (usegalaxy.eu): 577184 + No. of tool users (5 years) (usegalaxy.org): 43900 + No. of tool users (5 years) (usegalaxy.org.au): 2190 + No. of tool users (5 years) - all main servers: 623274 + No. of tool users (all time) (usegalaxy.eu): 577312 + No. of tool users (all time) (usegalaxy.org): 44233 + No. of tool users (all time) (usegalaxy.org.au): 2190 + No. of tool users (all time) - all main servers: 623735 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 463 + Tool usage (5 years) (usegalaxy.org): 283 + Tool usage (5 years) (usegalaxy.org.au): 112 + Tool usage (5 years) - all main servers: 858 + Tool usage (all time) (usegalaxy.eu): 492 + Tool usage (all time) (usegalaxy.org): 373 + Tool usage (all time) (usegalaxy.org.au): 112 + Tool usage (all time) - all main servers: 977 + ToolShed categories: + - Text Manipulation + ToolShed id: replace_column_by_key_value_file + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: This tool fetches data from pubchem via the PubChem REST API. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pubchem_rest_tool + Galaxy wrapper id: rest_tool + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Data Source + ToolShed id: pubchem_rest_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: antarna + Conda version: 2.0.1.2 + Date of first commit of the suite: '2015-04-30' + Description: antaRNA uses ant colony optimization to solve the inverse folding problem + in RNA research . + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - antarna + Galaxy wrapper id: antarna + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 292 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 292 + No. of tool users (all time) (usegalaxy.eu): 306 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 306 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - RNA + ToolShed id: antarna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2017-02-01' + Description: AREsite2 REST Interface + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - AREsite2_REST + Galaxy wrapper id: aresite2 + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 59 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 59 + No. of tool users (all time) (usegalaxy.eu): 74 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 74 + Source: http://rna.tbi.univie.ac.at/AREsite + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 10 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - RNA + - Data Source + - Sequence Analysis + ToolShed id: aresite2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: blockclust + Conda version: 1.1.1 + Date of first commit of the suite: '2015-02-28' + Description: BlockClust detects transcripts with similar processing patterns. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - blockclust + Galaxy wrapper id: blockclust + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust + Galaxy wrapper version: 1.1.1 + No. of tool users (5 years) (usegalaxy.eu): 811 + No. of tool users (5 years) (usegalaxy.org): 64 + No. of tool users (5 years) (usegalaxy.org.au): 561 + No. of tool users (5 years) - all main servers: 1436 + No. of tool users (all time) (usegalaxy.eu): 1501 + No. of tool users (all time) (usegalaxy.org): 64 + No. of tool users (all time) (usegalaxy.org.au): 561 + No. of tool users (all time) - all main servers: 2126 + Source: https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 54 + Tool usage (5 years) (usegalaxy.org): 29 + Tool usage (5 years) (usegalaxy.org.au): 15 + Tool usage (5 years) - all main servers: 98 + Tool usage (all time) (usegalaxy.eu): 79 + Tool usage (all time) (usegalaxy.org): 29 + Tool usage (all time) (usegalaxy.org.au): 15 + Tool usage (all time) - all main servers: 123 + ToolShed categories: + - RNA + ToolShed id: blockclust + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl + Conda version: null + Date of first commit of the suite: '2023-08-19' + Description: removes lower scoring overlaps from cmsearch results. + EDAM operation: + - Comparison + - Alignment + EDAM operation (no superclasses): + - Comparison + - Alignment + EDAM topic: + - Biology + - Medicine + EDAM topic (no superclasses): + - Biology + - Medicine + Galaxy tool ids: + - cmsearch_deoverlap + Galaxy wrapper id: cmsearch_deoverlap + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap + Galaxy wrapper version: 0.08+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 2609 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2609 + No. of tool users (all time) (usegalaxy.eu): 2609 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2609 + Source: https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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cmsearch-deoverlap + bio.tool name: cmsearch-deoverlap +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cmv + Conda version: 1.0.8 + Date of first commit of the suite: '2017-09-26' + Description: cmv is a collection of tools for the visualisation of Hidden Markov + Models and RNA-family models. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cmcv + - cmv + - hmmcv + - hmmv + Galaxy wrapper id: cmv + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv + Galaxy wrapper version: 1.0.8 + No. of tool users (5 years) (usegalaxy.eu): 90 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - 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cofold + Galaxy wrapper id: cofold + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold + Galaxy wrapper version: 2.0.4.0 + No. of tool users (5 years) (usegalaxy.eu): 316 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 316 + No. of tool users (all time) (usegalaxy.eu): 355 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 355 + Source: http://www.e-rna.org/cofold/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 25 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 25 + Tool usage (all time) (usegalaxy.eu): 29 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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exparna + Galaxy wrapper id: exparna + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - RNA + ToolShed id: exparna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: graphprot + Conda version: 1.1.7 + Date of first commit of the suite: '2018-05-25' + Description: GraphProt models binding preferences of RNA-binding proteins. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - graphprot_predict_profile + Galaxy wrapper id: graphprot + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot + Galaxy wrapper version: 1.1.7+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 463 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 463 + No. of tool users (all time) (usegalaxy.eu): 484 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 484 + Source: https://github.com/dmaticzka/GraphProt + Status: To update + Tool usage (5 years) (usegalaxy.eu): 18 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 18 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 19 + ToolShed categories: + - Sequence Analysis + - RNA + - CLIP-seq + ToolShed id: graphprot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: htseq-clip + Conda version: 2.19.0b0 + Date of first commit of the suite: '2022-10-11' + Description: htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - htseq_clip + Galaxy wrapper id: htseq-clip + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip + Galaxy wrapper version: 0.1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 98 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 98 + No. of tool users (all time) (usegalaxy.eu): 98 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 98 + Source: https://github.com/EMBL-Hentze-group/htseq-clip + Status: To update + Tool usage (5 years) (usegalaxy.eu): 19 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 19 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 19 + ToolShed categories: + - Sequence Analysis + - RNA + - CLIP-seq + ToolShed id: htseq_clip + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 6 + Conda id: infernal + Conda version: 1.1.5 + Date of first commit of the suite: '2015-05-07' + Description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence + databases for RNA structure and sequence similarities. + EDAM operation: + - Nucleic acid feature detection + EDAM operation (no superclasses): + - Nucleic acid feature detection + EDAM topic: + - Sequence sites, features and motifs + - Structural genomics + EDAM topic (no superclasses): + - Sequence sites, features and motifs + - Structural genomics + Galaxy tool ids: + - infernal_cmalign + - infernal_cmbuild + - infernal_cmpress + - infernal_cmscan + - infernal_cmsearch + - infernal_cmstat + Galaxy wrapper id: infernal + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/infernal + Galaxy wrapper version: 1.1.4 + No. of tool users (5 years) (usegalaxy.eu): 59700 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1157 + No. of tool users (5 years) - all main servers: 60857 + No. of tool users (all time) (usegalaxy.eu): 112582 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1221 + No. of tool users (all time) - all main servers: 113803 + Source: http://infernal.janelia.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 223 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 34 + Tool usage (5 years) - all main servers: 257 + Tool usage (all time) (usegalaxy.eu): 282 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 35 + Tool usage (all time) - all main servers: 317 + ToolShed categories: + - RNA + ToolShed id: infernal + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 6 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 6 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.no: 6 + UseGalaxy.or: 6 + biii: null + bio.tool description: Infernal ("INFERence of RNA ALignment") is for searching DNA + sequence databases for RNA structure and sequence similarities. It is an implementation + of a special case of profile stochastic context-free grammars called covariance + models (CMs). A CM is like a sequence profile, but it scores a combination of + sequence consensus and RNA secondary structure consensus, so in many cases, it + is more capable of identifying RNA homologs that conserve their secondary structure + more than their primary sequence. + bio.tool id: infernal + bio.tool ids: + - infernal + bio.tool name: Infernal +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: INFO-RNA is a service for the design of RNA sequences that fold into + a given pseudo-knot free RNA secondary structure. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: [] + Galaxy wrapper id: inforna + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - RNA + ToolShed id: inforna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: intarna + Conda version: 3.4.1 + Date of first commit of the suite: '2019-01-10' + Description: Efficient RNA-RNA interaction prediction incorporating accessibility + and seeding of interaction sites. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - intarna + Galaxy wrapper id: intarna + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna + Galaxy wrapper version: 3.4.1 + No. of tool users (5 years) (usegalaxy.eu): 3071 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3071 + No. of tool users (all time) (usegalaxy.eu): 7652 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7652 + Source: https://github.com/BackofenLab/IntaRNA + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 41 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 41 + Tool usage (all time) (usegalaxy.eu): 47 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 47 + ToolShed categories: + - RNA + ToolShed id: intarna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Kinwalker splits the folding process into a series of events where + each event can either be a folding event or a transcription event. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: [] + Galaxy wrapper id: kinwalker + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - RNA + ToolShed id: kinwalker + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: locarna + Conda version: 2.0.1 + Date of first commit of the suite: '2015-02-28' + Description: LocARNA - A suite for multiple alignment and folding of RNAs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - locarna_exparnap + - locarna_multiple + - locarna_pairwise + - locarna_pairwise_p + - locarna_reliability_profile + Galaxy wrapper id: locarna + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna + Galaxy wrapper version: 2.0.1 + No. of tool users (5 years) (usegalaxy.eu): 314 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 314 + No. of tool users (all time) (usegalaxy.eu): 350 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 350 + Source: http://www.bioinf.uni-freiburg.de/Software/LocARNA/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 36 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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mea + Galaxy wrapper id: mea + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea + Galaxy wrapper version: 0.6.4.1 + No. of tool users (5 years) (usegalaxy.eu): 73 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 73 + No. of tool users (all time) (usegalaxy.eu): 86 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 86 + Source: http://www.bioinf.uni-leipzig.de/Software/mea + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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paralyzer + Galaxy wrapper id: paralyzer + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer + Galaxy wrapper version: '1.5' + No. of tool users (5 years) (usegalaxy.eu): 322 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 322 + No. of tool users (all time) (usegalaxy.eu): 349 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 349 + Source: https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 24 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 24 + Tool usage (all time) (usegalaxy.eu): 29 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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RNA + - Protein interactions + - RNA immunoprecipitation + - Bioinformatics + - Sequence analysis + EDAM topic (no superclasses): + - RNA + - Protein interactions + - RNA immunoprecipitation + - Bioinformatics + - Sequence analysis + Galaxy tool ids: + - rbpbench + Galaxy wrapper id: rbpbench + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench + Galaxy wrapper version: 0.8.1 + No. of tool users (5 years) (usegalaxy.eu): 90 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 90 + No. of tool users (all time) (usegalaxy.eu): 90 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 90 + Source: https://github.com/michauhl/RBPBench + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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rbpbench + bio.tool name: RBPBench +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-rcas + Conda version: 1.28.2 + Date of first commit of the suite: '2017-04-13' + Description: RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide + regions detected by high-throughput experiments + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rcas + Galaxy wrapper id: rcas + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ + Galaxy wrapper version: 1.5.4 + No. of tool users (5 years) (usegalaxy.eu): 860 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 860 + No. of tool users (all time) (usegalaxy.eu): 1257 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1257 + Source: https://github.com/BIMSBbioinfo/RCAS + Status: To update + Tool usage (5 years) (usegalaxy.eu): 88 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 88 + Tool usage (all time) (usegalaxy.eu): 98 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 98 + ToolShed categories: + - RNA + ToolShed id: rcas + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: reago + Conda version: '1.1' + Date of first commit of the suite: '2015-12-09' + Description: Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic + data. + EDAM operation: + - Sequence assembly + EDAM operation (no superclasses): + - Sequence assembly + EDAM topic: + - Sequence assembly + - RNA + - Metagenomics + - Microbiology + EDAM topic (no superclasses): + - Sequence assembly + - RNA + - Metagenomics + - Microbiology + Galaxy tool ids: + - reago + Galaxy wrapper id: reago + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/chengyuan/reago-1.1 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + - RNA + ToolShed id: reago + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: This is an assembly tool for 16S ribosomal RNA recovery from + metagenomic data. + bio.tool id: reago + bio.tool ids: + - reago + bio.tool name: REAGO +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: remurna + Conda version: '1.0' + Date of first commit of the suite: '2016-11-24' + Description: remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes + of RNA Conformation + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - remurna + Galaxy wrapper id: remurna + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 39 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 39 + No. of tool users (all time) (usegalaxy.eu): 44 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 44 + Source: https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - RNA + ToolShed id: remurna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ribotaper + Conda version: 1.3.1 + Date of first commit of the suite: '2016-03-23' + Description: A method for defining traslated ORFs using Ribosome Profiling data. + EDAM operation: + - Gene expression profiling + EDAM operation (no superclasses): + - Gene expression profiling + EDAM topic: + - Functional genomics + EDAM topic (no superclasses): + - Functional genomics + Galaxy tool ids: + - ribotaper_create_annotation + - ribotaper_create_metaplots + - ribotaper_ribosome_profiling + Galaxy wrapper id: ribotaper + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ + Galaxy wrapper version: 1.3.1a + No. of tool users (5 years) (usegalaxy.eu): 661 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 661 + No. of tool users (all time) (usegalaxy.eu): 681 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 681 + Source: https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 78 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 78 + Tool usage (all time) (usegalaxy.eu): 78 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 78 + ToolShed categories: + - RNA + ToolShed id: ribotaper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.no: 3 + biii: null + bio.tool description: New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, + which exploits the triplet periodicity of ribosomal footprints to call translated + regions. + bio.tool id: ribotaper + bio.tool ids: + - ribotaper + bio.tool name: RiboTaper +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: '@EXECUTABLE@' + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Compute secondary structures of RNA + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - RNAshapes + Galaxy wrapper id: rna_shapes + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes + Galaxy wrapper version: 3.3.0 + No. of tool users (5 years) (usegalaxy.eu): 137 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 137 + No. of tool users (all time) (usegalaxy.eu): 173 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 173 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 40 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 40 + Tool usage (all time) (usegalaxy.eu): 49 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 49 + ToolShed categories: + - RNA + ToolShed id: rnashapes + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rnabob + Conda version: 2.2.1 + Date of first commit of the suite: '2015-02-28' + Description: Fast pattern searching for RNA structural motifs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rbc_rnabob + Galaxy wrapper id: rnabob + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob + Galaxy wrapper version: 2.2.1.0 + No. of tool users (5 years) (usegalaxy.eu): 90 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 90 + No. of tool users (all time) (usegalaxy.eu): 196 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 196 + Source: http://eddylab.org/software.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - RNA + ToolShed id: rnabob + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rnacode + Conda version: '0.3' + Date of first commit of the suite: '2015-06-16' + Description: Analyze the protein coding potential in MSA + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rbc_rnacode + Galaxy wrapper id: rnacode + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode + Galaxy wrapper version: 0.3.2 + No. of tool users (5 years) (usegalaxy.eu): 878 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 878 + No. of tool users (all time) (usegalaxy.eu): 1363 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1363 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 29 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 29 + Tool usage (all time) (usegalaxy.eu): 35 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 35 + ToolShed categories: + - RNA + ToolShed id: rnacode + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: sam + Conda version: '3.5' + Date of first commit of the suite: '2016-05-31' + Description: RNAcommender is a tool for genome-wide recommendation of RNA-protein + interactions. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rbc_rnacommender + Galaxy wrapper id: rnacommender + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender + Galaxy wrapper version: 0.1.1 + No. of tool users (5 years) (usegalaxy.eu): 1024 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1024 + No. of tool users (all time) (usegalaxy.eu): 1077 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1077 + Source: https://github.com/gianlucacorrado/RNAcommender + Status: To update + Tool usage (5 years) (usegalaxy.eu): 18 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 18 + Tool usage (all time) (usegalaxy.eu): 21 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 21 + ToolShed categories: + - RNA + ToolShed id: rnacommender + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rnaformer + Conda version: null + Date of first commit of the suite: '2024-07-11' + Description: 'RNAformer: RNA secondary structure prediction' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - infer_rnaformer + Galaxy wrapper id: rnaformer + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 26 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 26 + No. of tool users (all time) (usegalaxy.eu): 26 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 26 + Source: https://github.com/automl/RNAformer + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - RNA + ToolShed id: rnaformer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rnalien + Conda version: 1.8.0 + Date of first commit of the suite: '2017-03-07' + Description: RNAlien unsupervized RNA family model construction + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - RNAlien + Galaxy wrapper id: rnalien + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien + Galaxy wrapper version: 1.3.6 + No. of tool users (5 years) (usegalaxy.eu): 23 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 23 + No. of tool users (all time) (usegalaxy.eu): 33 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 33 + Source: http://rna.tbi.univie.ac.at/rnalien/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 10 + Tool usage (all time) (usegalaxy.eu): 14 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 14 + ToolShed categories: + - RNA + - Sequence Analysis + ToolShed id: rnalien + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rnasnp + Conda version: '1.2' + Date of first commit of the suite: '2016-11-24' + Description: RNAsnp Efficient detection of local RNA secondary structure changes + induced by SNPs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rnasnp + Galaxy wrapper id: rnasnp + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 65 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 65 + No. of tool users (all time) (usegalaxy.eu): 89 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 89 + Source: http://rth.dk/resources/rnasnp/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 14 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 14 + Tool usage (all time) (usegalaxy.eu): 18 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 18 + ToolShed categories: + - RNA + ToolShed id: rnasnp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rnaz + Conda version: 2.1.1 + Date of first commit of the suite: '2016-10-22' + Description: RNAz is a program for predicting structurally conserved and thermodynamically + stable RNA secondary structures in multiple sequence alignments. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rnaz + - rnaz_annotate + - rnaz_cluster + - rnaz_randomize_aln + - rnaz_select_seqs + - rnaz_window + Galaxy wrapper id: rnaz + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz + Galaxy wrapper version: 2.1.1 + No. of tool users (5 years) (usegalaxy.eu): 1156 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1156 + No. of tool users (all time) (usegalaxy.eu): 43309 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 43309 + Source: https://www.tbi.univie.ac.at/~wash/RNAz/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 93 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 93 + Tool usage (all time) (usegalaxy.eu): 121 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 121 + ToolShed categories: + - RNA + ToolShed id: rnaz + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 6 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.no: 6 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: selectsequencesfrommsa + Conda version: 1.0.5 + Date of first commit of the suite: '2017-03-11' + Description: SelectSequences - selects representative entries from a multiple sequence + alignment in clustal format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - selectsequencesfrommsa + Galaxy wrapper id: selectsequencesfrommsa + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa + Galaxy wrapper version: 1.0.5 + No. of tool users (5 years) (usegalaxy.eu): 305 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 305 + No. of tool users (all time) (usegalaxy.eu): 463 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 463 + Source: https://github.com/eggzilla/SelectSequences + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 43 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 43 + Tool usage (all time) (usegalaxy.eu): 50 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 50 + ToolShed categories: + - RNA + - Sequence Analysis + ToolShed id: selectsequencesfrommsa + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: sortmerna + Conda version: 4.3.7 + Date of first commit of the suite: '2016-03-17' + Description: SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments + from metatransriptomic data produced by next-generation sequencers. + EDAM operation: + - Sequence similarity search + - Sequence comparison + - Sequence alignment analysis + EDAM operation (no superclasses): + - Sequence similarity search + - Sequence alignment analysis + EDAM topic: + - Metatranscriptomics + - Metagenomics + EDAM topic (no superclasses): + - Metatranscriptomics + - Metagenomics + Galaxy tool ids: + - bg_sortmerna + Galaxy wrapper id: sortmerna + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna + Galaxy wrapper version: 4.3.6 + No. of tool users (5 years) (usegalaxy.eu): 19865 + No. of tool users (5 years) (usegalaxy.org): 3141 + No. of tool users (5 years) (usegalaxy.org.au): 3304 + No. of tool users (5 years) - all main servers: 26310 + No. of tool users (all time) (usegalaxy.eu): 21034 + No. of tool users (all time) (usegalaxy.org): 3141 + No. of tool users (all time) (usegalaxy.org.au): 3304 + No. of tool users (all time) - all main servers: 27479 + Source: http://bioinfo.lifl.fr/RNA/sortmerna/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1047 + Tool usage (5 years) (usegalaxy.org): 328 + Tool usage (5 years) (usegalaxy.org.au): 189 + Tool usage (5 years) - all main servers: 1564 + Tool usage (all time) (usegalaxy.eu): 1126 + Tool usage (all time) (usegalaxy.org): 328 + Tool usage (all time) (usegalaxy.org.au): 189 + Tool usage (all time) - all main servers: 1643 + ToolShed categories: + - RNA + ToolShed id: sortmerna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Sequence analysis tool for filtering, mapping and OTU-picking + NGS reads. + bio.tool id: sortmerna + bio.tool ids: + - sortmerna + bio.tool name: SortMeRNA +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: sshmm + Conda version: 1.0.7 + Date of first commit of the suite: '2018-07-05' + Description: ssHMM is an RNA sequence-structure motif finder for RNA-binding protein + data, such as CLIP-Seq data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sshmm + Galaxy wrapper id: sshmm + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ + Galaxy wrapper version: 1.0.7 + No. of tool users (5 years) (usegalaxy.eu): 214 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 214 + No. of tool users (all time) (usegalaxy.eu): 225 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 225 + Source: https://github.molgen.mpg.de/heller/ssHMM + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 18 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 18 + ToolShed categories: + - Sequence Analysis + - RNA + ToolShed id: sshmm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: targetfinder + Conda version: '1.7' + Date of first commit of the suite: '2015-10-23' + Description: Plant small RNA target prediction tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - targetfinder + Galaxy wrapper id: targetfinder + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ + Galaxy wrapper version: '1.7' + No. of tool users (5 years) (usegalaxy.eu): 827 + No. of tool users (5 years) (usegalaxy.org): 114 + No. of tool users (5 years) (usegalaxy.org.au): 900 + No. of tool users (5 years) - all main servers: 1841 + No. of tool users (all time) (usegalaxy.eu): 838 + No. of tool users (all time) (usegalaxy.org): 114 + No. of tool users (all time) (usegalaxy.org.au): 900 + No. of tool users (all time) - all main servers: 1852 + Source: https://github.com/carringtonlab/TargetFinder.git + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 89 + Tool usage (5 years) (usegalaxy.org): 41 + Tool usage (5 years) (usegalaxy.org.au): 29 + Tool usage (5 years) - all main servers: 159 + Tool usage (all time) (usegalaxy.eu): 92 + Tool usage (all time) (usegalaxy.org): 41 + Tool usage (all time) (usegalaxy.org.au): 29 + Tool usage (all time) - all main servers: 162 + ToolShed categories: + - RNA + ToolShed id: targetfinder + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 2 + Conda id: aragorn + Conda version: 1.2.41 + Date of first commit of the suite: '2015-05-08' + Description: Aragorn predicts tRNA and tmRNA in nucleotide sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - aragorn_trna + - trnascan + Galaxy wrapper id: trna_prediction + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction + Galaxy wrapper version: '0.6' + No. of tool users (5 years) (usegalaxy.eu): 4361 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 2469 + No. of tool users (5 years) - all main servers: 6830 + No. of tool users (all time) (usegalaxy.eu): 4601 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 2469 + No. of tool users (all time) - all main servers: 7070 + Source: http://mbioserv2.mbioekol.lu.se/ARAGORN/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 741 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 190 + Tool usage (5 years) - all main servers: 931 + Tool usage (all time) (usegalaxy.eu): 807 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 190 + Tool usage (all time) - all main servers: 997 + ToolShed categories: + - RNA + ToolShed id: trna_prediction + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 21 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: viennarna + Conda version: 2.6.4 + Date of first commit of the suite: '2017-08-19' + Description: ViennaRNA - Prediction and comparison of RNA secondary structures + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - viennarna_kinfold + - viennarna_kinwalker + - viennarna_rna2dfold + - viennarna_rnaaliduplex + - viennarna_rnaalifold + - viennarna_rnacofold + - viennarna_rnadistance + - viennarna_rnaduplex + - viennarna_rnaeval + - viennarna_rnafold + - viennarna_rnaheat + - viennarna_rnainverse + - viennarna_rnalalifold + - viennarna_rnalfold + - viennarna_rnapaln + - viennarna_rnadpdist + - viennarna_rnapkplex + - viennarna_rnaplex + - viennarna_rnaplfold + - viennarna_rnaplot + - viennarna_rnasnoop + - viennarna_rnasubopt + - viennarna_rnaup + Galaxy wrapper id: vienna_rna + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna + Galaxy wrapper version: 2.2.10 + No. of tool users (5 years) (usegalaxy.eu): 3197 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3197 + No. of tool users (all time) (usegalaxy.eu): 8107 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8107 + Source: http://www.tbi.univie.ac.at/RNA/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 344 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 344 + Tool usage (all time) (usegalaxy.eu): 415 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 415 + ToolShed categories: + - RNA + ToolShed id: viennarna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 21 + Tools available on UseGalaxy.eu: 21 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 21 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 21 + UseGalaxy.eu: 21 + UseGalaxy.no: 21 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bzip2 + Conda version: null + Date of first commit of the suite: '2015-09-05' + Description: Sailfish is a tool for transcript quantification from RNA-seq data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sailfish + Galaxy wrapper id: sailfish + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish + Galaxy wrapper version: 0.10.1.1 + No. of tool users (5 years) (usegalaxy.eu): 3628 + No. of tool users (5 years) (usegalaxy.org): 8399 + No. of tool users (5 years) (usegalaxy.org.au): 2710 + No. of tool users (5 years) - all main servers: 14737 + No. of tool users (all time) (usegalaxy.eu): 4168 + No. of tool users (all time) (usegalaxy.org): 14473 + No. of tool users (all time) (usegalaxy.org.au): 3000 + No. of tool users (all time) - all main servers: 21641 + Source: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 165 + Tool usage (5 years) (usegalaxy.org): 573 + Tool usage (5 years) (usegalaxy.org.au): 151 + Tool usage (5 years) - all main servers: 889 + Tool usage (all time) (usegalaxy.eu): 199 + Tool usage (all time) (usegalaxy.org): 1147 + Tool usage (all time) (usegalaxy.org.au): 175 + Tool usage (all time) - all main servers: 1521 + ToolShed categories: + - Sequence Analysis + - RNA + ToolShed id: sailfish + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: salmon + Conda version: 1.10.3 + Date of first commit of the suite: '2019-09-18' + Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level + quantification estimates from RNA-seq and single-cell data. + EDAM operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + EDAM operation (no superclasses): + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + EDAM topic: + - RNA-Seq + - Gene expression + - Transcriptomics + EDAM topic (no superclasses): + - RNA-Seq + - Transcriptomics + Galaxy tool ids: + - alevin + - salmon + - salmonquantmerge + Galaxy wrapper id: salmon + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/salmon + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/salmon + Galaxy wrapper version: 1.10.1 + No. of tool users (5 years) (usegalaxy.eu): 73085 + No. of tool users (5 years) (usegalaxy.org): 90634 + No. of tool users (5 years) (usegalaxy.org.au): 13371 + No. of tool users (5 years) - all main servers: 177090 + No. of tool users (all time) (usegalaxy.eu): 77081 + No. of tool users (all time) (usegalaxy.org): 122835 + No. of tool users (all time) (usegalaxy.org.au): 15818 + No. of tool users (all time) - all main servers: 215734 + Source: https://github.com/COMBINE-lab/salmon + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2243 + Tool usage (5 years) (usegalaxy.org): 3402 + Tool usage (5 years) (usegalaxy.org.au): 513 + Tool usage (5 years) - all main servers: 6158 + Tool usage (all time) (usegalaxy.eu): 2319 + Tool usage (all time) (usegalaxy.org): 4726 + Tool usage (all time) (usegalaxy.org.au): 586 + Tool usage (all time) - all main servers: 7631 + ToolShed categories: + - Sequence Analysis + - RNA + - Transcriptomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 2 + UseGalaxy.no: 3 + UseGalaxy.or: 2 + biii: null + bio.tool description: A tool for transcript expression quantification from RNA-seq + data + bio.tool id: salmon + bio.tool ids: + - salmon + bio.tool name: Salmon +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: sambamba + Conda version: 1.0.1 + Date of first commit of the suite: '2016-06-23' + Description: 'Sambamba: process your BAM data faster!' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sambamba_flagstat + - sambamba_markdup + - sambamba_merge + - sambamba_sort + Galaxy wrapper id: sambamba + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/sambamba + Galaxy wrapper source: https://github.com/biod/sambamba + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 297 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 297 + No. of tool users (all time) (usegalaxy.eu): 297 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 297 + Source: https://github.com/biod/sambamba + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 51 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 51 + Tool usage (all time) (usegalaxy.eu): 51 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 51 + ToolShed categories: + - SAM + ToolShed id: sambamba + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: sed + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Manipulate your data with the sed command line tool. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sed_stream_editor + Galaxy wrapper id: sed + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/sed + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/sed + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 281 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 281 + No. of tool users (all time) (usegalaxy.eu): 2284 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2284 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/sed + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 10 + Tool usage (all time) (usegalaxy.eu): 53 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 53 + ToolShed categories: + - Text Manipulation + ToolShed id: sed_wrapper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: segemehl + Conda version: 0.3.4 + Date of first commit of the suite: '2015-02-28' + Description: segemehl - short read mapping with gaps + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - segemehl + Galaxy wrapper id: segemehl + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/segemehl + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/segemehl + Galaxy wrapper version: 0.2.0.4 + No. of tool users (5 years) (usegalaxy.eu): 1095 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1095 + No. of tool users (all time) (usegalaxy.eu): 1306 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1306 + Source: http://www.bioinf.uni-leipzig.de/Software/segemehl/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 98 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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sklearn_mlxtend_association_rules + - sklearn_clf_metrics + - sklearn_discriminant_classifier + - sklearn_ensemble + - sklearn_estimator_attributes + - sklearn_feature_selection + - sklearn_fitted_model_eval + - sklearn_generalized_linear + - keras_batch_models + - keras_model_builder + - keras_model_config + - keras_train_and_eval + - sklearn_label_encoder + - sklearn_lightgbm + - ml_visualization_ex + - model_prediction + - sklearn_model_validation + - sklearn_nn_classifier + - sklearn_numeric_clustering + - sklearn_pairwise_metrics + - sklearn_pca + - sklearn_build_pipeline + - sklearn_data_preprocess + - sklearn_regression_metrics + - sklearn_sample_generator + - sklearn_searchcv + - sklearn_model_fit + - scipy_sparse + - stacking_ensemble_models + - sklearn_svm_classifier + - sklearn_to_categorical + - sklearn_train_test_eval + - sklearn_train_test_split + Galaxy wrapper id: sklearn + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/sklearn + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/sklearn + Galaxy wrapper version: 1.0.11.0 + No. of tool users (5 years) (usegalaxy.eu): 82169 + No. of tool users (5 years) (usegalaxy.org): 18101 + No. of tool users (5 years) (usegalaxy.org.au): 17549 + No. of tool users (5 years) - 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rbc_splitfasta + Galaxy wrapper id: splitfasta + Galaxy wrapper owner: rnateam + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta + Galaxy wrapper version: 0.4.0 + No. of tool users (5 years) (usegalaxy.eu): 1772 + No. of tool users (5 years) (usegalaxy.org): 3012 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4784 + No. of tool users (all time) (usegalaxy.eu): 1811 + No. of tool users (all time) (usegalaxy.org): 3012 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4823 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 278 + Tool usage (5 years) (usegalaxy.org): 564 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 842 + Tool usage (all time) (usegalaxy.eu): 294 + Tool usage (all time) (usegalaxy.org): 564 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 858 + ToolShed categories: + - Text Manipulation + ToolShed id: splitfasta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2015-02-28' + Description: Tool for computing statistical tests. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bg_statistical_hypothesis_testing + Galaxy wrapper id: statistics + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/statistics + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/statistics + Galaxy wrapper version: '0.3' + No. of tool users (5 years) (usegalaxy.eu): 169 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 169 + No. of tool users (all time) (usegalaxy.eu): 346 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 346 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/statistics + Status: To update + Tool usage (5 years) (usegalaxy.eu): 46 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 46 + Tool usage (all time) (usegalaxy.eu): 61 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 61 + ToolShed categories: + - Statistics + ToolShed id: bg_statistical_hypothesis_testing + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: stress-ng + Conda version: null + Date of first commit of the suite: '2021-03-04' + Description: stress test a computer system in various selectable ways + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - stress_ng + Galaxy wrapper id: stress_ng + Galaxy wrapper owner: bgruening-util + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng + Galaxy wrapper source: https://github.com/ColinIanKing/stress-ng + Galaxy wrapper version: 0.12.04 + No. of tool users (5 years) (usegalaxy.eu): 62 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 62 + No. of tool users (all time) (usegalaxy.eu): 62 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 62 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 3 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Web Services + ToolShed id: stress_ng + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hmmer + Conda version: '3.4' + Date of first commit of the suite: '2024-02-14' + Description: Search for transcription associated proteins (TAPs) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tapscan_classify + Galaxy wrapper id: tapscan + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/tapscan + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/tapscan + Galaxy wrapper version: 4.76+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 19 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 19 + No. of tool users (all time) (usegalaxy.eu): 19 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 19 + Source: https://plantcode.cup.uni-freiburg.de/tapscan/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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all main servers: 620 + ToolShed categories: + - Text Manipulation + ToolShed id: add_line_to_file + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-03-02' + Description: Column arrange by header name + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bg_column_arrange_by_header + Galaxy wrapper id: column_arrange_by_header + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header + Galaxy wrapper version: '0.2' + No. of tool users (5 years) (usegalaxy.eu): 5356 + No. of tool users (5 years) (usegalaxy.org): 2026 + No. of tool users (5 years) (usegalaxy.org.au): 1400 + No. of tool users (5 years) - all main servers: 8782 + No. of tool users (all time) (usegalaxy.eu): 5636 + No. of tool users (all time) (usegalaxy.org): 2026 + No. of tool users (all time) (usegalaxy.org.au): 1531 + No. of tool users (all time) - all main servers: 9193 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 446 + Tool usage (5 years) (usegalaxy.org): 375 + Tool usage (5 years) (usegalaxy.org.au): 117 + Tool usage (5 years) - 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join_files_on_column_fuzzy + Galaxy wrapper id: join_files_on_column_fuzzy + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 1980 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1081 + No. of tool users (5 years) - all main servers: 3061 + No. of tool users (all time) (usegalaxy.eu): 2697 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1081 + No. of tool users (all time) - all main servers: 3778 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 345 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 44 + Tool usage (5 years) - 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tp_split_on_column + Galaxy wrapper id: split_file_on_column + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column + Galaxy wrapper version: '0.6' + No. of tool users (5 years) (usegalaxy.eu): 5995 + No. of tool users (5 years) (usegalaxy.org): 2150 + No. of tool users (5 years) (usegalaxy.org.au): 26 + No. of tool users (5 years) - all main servers: 8171 + No. of tool users (all time) (usegalaxy.eu): 6261 + No. of tool users (all time) (usegalaxy.org): 2150 + No. of tool users (all time) (usegalaxy.org.au): 26 + No. of tool users (all time) - all main servers: 8437 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 408 + Tool usage (5 years) (usegalaxy.org): 311 + Tool usage (5 years) (usegalaxy.org.au): 2 + Tool usage (5 years) - all main servers: 721 + Tool usage (all time) (usegalaxy.eu): 453 + Tool usage (all time) (usegalaxy.org): 311 + Tool usage (all time) (usegalaxy.org.au): 2 + Tool usage (all time) - all main servers: 766 + ToolShed categories: + - Text Manipulation + ToolShed id: split_file_on_column + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-08-28' + Description: Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - split_file_to_collection + Galaxy wrapper id: split_file_to_collection + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection + Galaxy wrapper version: 0.5.2 + No. of tool users (5 years) (usegalaxy.eu): 16415 + No. of tool users (5 years) (usegalaxy.org): 9133 + No. of tool users (5 years) (usegalaxy.org.au): 4140 + No. of tool users (5 years) - all main servers: 29688 + No. of tool users (all time) (usegalaxy.eu): 16623 + No. of tool users (all time) (usegalaxy.org): 9133 + No. of tool users (all time) (usegalaxy.org.au): 4140 + No. of tool users (all time) - all main servers: 29896 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection + Status: To update + Tool usage (5 years) (usegalaxy.eu): 968 + Tool usage (5 years) (usegalaxy.org): 672 + Tool usage (5 years) (usegalaxy.org.au): 148 + Tool usage (5 years) - all main servers: 1788 + Tool usage (all time) (usegalaxy.eu): 984 + Tool usage (all time) (usegalaxy.org): 672 + Tool usage (all time) (usegalaxy.org.au): 148 + Tool usage (all time) - all main servers: 1804 + ToolShed categories: + - Text Manipulation + ToolShed id: split_file_to_collection + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 20 + Available on UseGalaxy.fr: 20 + Available on UseGalaxy.org (Main): 20 + Available on UseGalaxy.org.au: 20 + Conda id: coreutils + Conda version: '8.25' + Date of first commit of the suite: '2019-01-12' + Description: High performance text processing tools using the GNU coreutils, sed, + awk and friends. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tp_awk_tool + - tp_cat + - tp_cut_tool + - tp_easyjoin_tool + - tp_find_and_replace + - tp_grep_tool + - tp_head_tool + - tp_multijoin_tool + - nl + - tp_text_file_with_recurring_lines + - tp_replace_in_column + - tp_replace_in_line + - tp_sed_tool + - tp_sort_header_tool + - tp_sort_rows + - tp_uniq_tool + - tp_tac + - tp_tail_tool + - tp_unfold_column_tool + - tp_sorted_uniq + Galaxy wrapper id: text_processing + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing + Galaxy wrapper version: '9.3' + No. of tool users (5 years) (usegalaxy.eu): 3898014 + No. of tool users (5 years) (usegalaxy.org): 648268 + No. of tool users (5 years) (usegalaxy.org.au): 103365 + No. of tool users (5 years) - all main servers: 4649647 + No. of tool users (all time) (usegalaxy.eu): 4015573 + No. of tool users (all time) (usegalaxy.org): 915282 + No. of tool users (all time) (usegalaxy.org.au): 105214 + No. of tool users (all time) - all main servers: 5036069 + Source: https://www.gnu.org/software/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 37698 + Tool usage (5 years) (usegalaxy.org): 47636 + Tool usage (5 years) (usegalaxy.org.au): 7778 + Tool usage (5 years) - all main servers: 93112 + Tool usage (all time) (usegalaxy.eu): 42095 + Tool usage (all time) (usegalaxy.org): 69828 + Tool usage (all time) (usegalaxy.org.au): 7953 + Tool usage (all time) - all main servers: 119876 + ToolShed categories: + - Text Manipulation + ToolShed id: text_processing + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 19 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 19 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 19 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 20 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 19 + Tools available on UseGalaxy.cz: 19 + Tools available on UseGalaxy.eu: 20 + Tools available on UseGalaxy.fr: 20 + Tools available on UseGalaxy.no: 19 + Tools available on UseGalaxy.org (Main): 20 + Tools available on UseGalaxy.org.au: 20 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 19 + UseGalaxy.cz: 19 + UseGalaxy.eu: 20 + UseGalaxy.fr: 20 + UseGalaxy.no: 19 + UseGalaxy.or: 20 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: tgsgapcloser + Conda version: 1.2.1 + Date of first commit of the suite: '2021-11-14' + Description: TGS-GapCloser uses error-prone long reads or preassembled contigs to + fill N-gap in the genome assembly. + EDAM operation: + - Genome assembly + - Read mapping + - Scaffolding + - Localised reassembly + EDAM operation (no superclasses): + - Genome assembly + - Read mapping + - Scaffolding + - Localised reassembly + EDAM topic: + - Sequencing + - Sequence assembly + - Phylogeny + - Transcription factors and regulatory sites + - Mapping + EDAM topic (no superclasses): + - Sequencing + - Sequence assembly + - Phylogeny + - Transcription factors and regulatory sites + - Mapping + Galaxy tool ids: + - tgsgapcloser + Galaxy wrapper id: tgsgapcloser + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser + Galaxy wrapper version: 1.0.3 + No. of tool users (5 years) (usegalaxy.eu): 547 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 547 + No. of tool users (all time) (usegalaxy.eu): 547 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 547 + Source: https://github.com/BGI-Qingdao/TGS-GapCloser + Status: To update + Tool usage (5 years) (usegalaxy.eu): 51 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 51 + Tool usage (all time) (usegalaxy.eu): 51 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 51 + ToolShed categories: + - Assembly + ToolShed id: tgsgapcloser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: TGS-GapCloser is a fast and accurately passing through the + Bermuda in large genome using error-prone third-generation long reads. + bio.tool id: TGS-GapCloser + bio.tool ids: + - TGS-GapCloser + bio.tool name: TGS-GapCloser +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: tiara + Conda version: null + Date of first commit of the suite: '2024-05-23' + Description: Tool for identification of eukaryotic sequences in the metagenomic + datasets. + EDAM operation: + - Genome comparison + - Data retrieval + - Variant calling + - Genome visualisation + - Structural variation detection + EDAM operation (no superclasses): + - Genome comparison + - Data retrieval + - Variant calling + - Genome visualisation + - Structural variation detection + EDAM topic: + - Sequencing + - Genomics + - DNA polymorphism + - DNA structural variation + EDAM topic (no superclasses): + - Sequencing + - Genomics + - DNA polymorphism + Galaxy tool ids: + - tiara + Galaxy wrapper id: tiara + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/tiara + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/tiara + Galaxy wrapper version: 1.0.3 + No. of tool users (5 years) (usegalaxy.eu): 15 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 15 + No. of tool users (all time) (usegalaxy.eu): 15 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 15 + Source: https://github.com/ibe-uw/tiara + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Metagenomics + - Sequence Analysis + ToolShed id: tiara + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Total Integrated Archive of Short-Read and Array (TIARA) database, + contains personal genomic information obtained from next generation sequencing + (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) + arrays. This database improves the accuracy of detecting personal genomic variations, + such as SNPs, short indels and structural variants (SVs). + bio.tool id: Tiara + bio.tool ids: + - Tiara + bio.tool name: TIARA +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-08-23' + Description: Create model to recommend tools + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - create_tool_recommendation_model + Galaxy wrapper id: tool_recommendation_model + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model + Galaxy wrapper version: 0.0.5 + No. of tool users (5 years) (usegalaxy.eu): 445 + No. of tool users (5 years) (usegalaxy.org): 71 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 516 + No. of tool users (all time) (usegalaxy.eu): 445 + No. of tool users (all time) (usegalaxy.org): 71 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 516 + Source: https://github.com/bgruening/galaxytools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 25 + Tool usage (5 years) (usegalaxy.org): 32 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 57 + Tool usage (all time) (usegalaxy.eu): 25 + Tool usage (all time) (usegalaxy.org): 32 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 57 + ToolShed categories: + - Machine Learning + ToolShed id: create_tool_recommendation_model + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: trim-galore + Conda version: 0.6.10 + Date of first commit of the suite: '2015-04-22' + Description: Trim Galore adaptive quality and adapter trimmer + EDAM operation: + - Sequence trimming + - Primer removal + - Read pre-processing + EDAM operation (no superclasses): + - Sequence trimming + - Primer removal + - Read pre-processing + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - trim_galore + Galaxy wrapper id: trim_galore + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore + Galaxy wrapper version: 0.6.7 + No. of tool users (5 years) (usegalaxy.eu): 229489 + No. of tool users (5 years) (usegalaxy.org): 228708 + No. of tool users (5 years) (usegalaxy.org.au): 22644 + No. of tool users (5 years) - all main servers: 480841 + No. of tool users (all time) (usegalaxy.eu): 275008 + No. of tool users (all time) (usegalaxy.org): 324716 + No. of tool users (all time) (usegalaxy.org.au): 23869 + No. of tool users (all time) - all main servers: 623593 + Source: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5733 + Tool usage (5 years) (usegalaxy.org): 11708 + Tool usage (5 years) (usegalaxy.org.au): 1439 + Tool usage (5 years) - all main servers: 18880 + Tool usage (all time) (usegalaxy.eu): 6500 + Tool usage (all time) (usegalaxy.org): 16638 + Tool usage (all time) (usegalaxy.org.au): 1527 + Tool usage (all time) - all main servers: 24665 + ToolShed categories: + - Sequence Analysis + - Fastq Manipulation + ToolShed id: trim_galore + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A wrapper tool around Cutadapt and FastQC to consistently + apply quality and adapter trimming to FastQ files, with some extra functionality + for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. + bio.tool id: trim_galore + bio.tool ids: + - trim_galore + bio.tool name: Trim Galore +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: requests + Conda version: null + Date of first commit of the suite: '2015-10-09' + Description: UniProt ID mapping and sequence retrieval + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - uniprot + Galaxy wrapper id: uniprot_rest_interface + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface + Galaxy wrapper version: '0.6' + No. of tool users (5 years) (usegalaxy.eu): 2117 + No. of tool users (5 years) (usegalaxy.org): 3111 + No. of tool users (5 years) (usegalaxy.org.au): 806 + No. of tool users (5 years) - all main servers: 6034 + No. of tool users (all time) (usegalaxy.eu): 2725 + No. of tool users (all time) (usegalaxy.org): 5779 + No. of tool users (all time) (usegalaxy.org.au): 806 + No. of tool users (all time) - all main servers: 9310 + Source: https://github.com/jdrudolph/uniprot + Status: To update + Tool usage (5 years) (usegalaxy.eu): 341 + Tool usage (5 years) (usegalaxy.org): 594 + Tool usage (5 years) (usegalaxy.org.au): 50 + Tool usage (5 years) - all main servers: 985 + Tool usage (all time) (usegalaxy.eu): 412 + Tool usage (all time) (usegalaxy.org): 1011 + Tool usage (all time) (usegalaxy.org.au): 50 + Tool usage (all time) - all main servers: 1473 + ToolShed categories: + - Proteomics + - Sequence Analysis + ToolShed id: uniprot_rest_interface + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: vt + Conda version: 2015.11.10 + Date of first commit of the suite: '2015-02-28' + Description: A tool set for short variant discovery in genetic sequence data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vt_@BINARY@ + - vt_@BINARY@ + Galaxy wrapper id: vt + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/vt + Galaxy wrapper source: https://github.com/atks/vt + Galaxy wrapper version: '0.2' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + - Variant Analysis + ToolShed id: vt + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-04-23' + Description: Transcribe audio or video files to text using the OpenAI Whisper. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - whisper + Galaxy wrapper id: whisper + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/whisper + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/whisper + Galaxy wrapper version: '20231117' + No. of tool users (5 years) (usegalaxy.eu): 96 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 96 + No. of tool users (all time) (usegalaxy.eu): 96 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 96 + Source: https://github.com/bgruening/galaxytools/tree/master/tools/whisper + Status: To update + Tool usage (5 years) (usegalaxy.eu): 13 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 13 + Tool usage (all time) (usegalaxy.eu): 13 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 13 + ToolShed categories: + - Machine Learning + ToolShed id: whisper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: wtdbg + Conda version: '2.5' + Date of first commit of the suite: '2018-06-12' + Description: WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. + EDAM operation: + - Genome assembly + - De-novo assembly + EDAM operation (no superclasses): + - Genome assembly + - De-novo assembly + EDAM topic: + - Sequence assembly + - Sequencing + EDAM topic (no superclasses): + - Sequence assembly + - Sequencing + Galaxy tool ids: + - wtdbg + Galaxy wrapper id: wtdbg + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg + Galaxy wrapper version: '2.5' + No. of tool users (5 years) (usegalaxy.eu): 1619 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1619 + No. of tool users (all time) (usegalaxy.eu): 1715 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1715 + Source: https://github.com/ruanjue/wtdbg2 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 337 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 337 + Tool usage (all time) (usegalaxy.eu): 376 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 376 + ToolShed categories: + - Assembly + ToolShed id: wtdbg + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Wtdbg2 is a de novo sequence assembler for long noisy reads + produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads + without error correction and then builds the consensus from intermediate assembly + output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome + at a speed tens of times faster than CANU and FALCON while producing contigs of + comparable base accuracy. + bio.tool id: wtdbg2 + bio.tool ids: + - wtdbg2 + bio.tool name: wtdbg2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: biopython + Conda version: '1.70' + Date of first commit of the suite: '2015-04-28' + Description: Thread nucleotides onto a protein alignment (back-translation) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - align_back_trans + Galaxy wrapper id: align_back_trans + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans + Galaxy wrapper version: 0.0.10 + No. of tool users (5 years) (usegalaxy.eu): 511 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 511 + No. of tool users (all time) (usegalaxy.eu): 541 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 541 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans + Status: To update + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 32 + Tool usage (all time) (usegalaxy.eu): 35 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 35 + ToolShed categories: + - Fasta Manipulation + - Sequence Analysis + ToolShed id: align_back_trans + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: biopython + Conda version: '1.70' + Date of first commit of the suite: '2014-11-19' + Description: Chromosome Diagrams using Biopython + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - chromosome_diagram + Galaxy wrapper id: chromosome_diagram + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram + Galaxy wrapper source: null + Galaxy wrapper version: 0.0.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Graphics + - Sequence Analysis + - Visualization + ToolShed id: chromosome_diagram + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: samtools + Conda version: '1.21' + Date of first commit of the suite: '2013-11-05' + Description: Galaxy wrapper for the CLC Assembly Cell suite from CLCBio + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - clc_assembler + - clc_mapper + Galaxy wrapper id: clc_assembly_cell + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell + Galaxy wrapper version: 0.0.7 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + - Next Gen Mappers + - SAM + ToolShed id: clc_assembly_cell + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: clinod + Conda version: '1.3' + Date of first commit of the suite: '2014-02-18' + Description: 'NoD: a Nucleolar localization sequence detector for eukaryotic and + viral proteins' + EDAM operation: + - Nucleic acid sequence analysis + EDAM operation (no superclasses): + - Nucleic acid sequence analysis + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - clinod + Galaxy wrapper id: clinod + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 548 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 548 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 548 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 548 + Source: http://www.compbio.dundee.ac.uk/www-nod/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 18 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 18 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 18 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 18 + ToolShed categories: + - Sequence Analysis + ToolShed id: clinod + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: The command line NoD predictor (clinod) can be run from the + command line to predict Nucleolar localization sequences (NoLSs) that are short + targeting sequences responsible for the localization of proteins to the nucleolus.The + predictor accepts a list of FASTA formatted sequences as an input and outputs + the NOLS predictions as a result.Please note that currently, JPred secondary structure + predictions are not supported by clinod. However, we are working on it. + bio.tool id: clinod + bio.tool ids: + - clinod + bio.tool name: clinod +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: samtools + Conda version: '1.21' + Date of first commit of the suite: '2016-02-05' + Description: Count sequence variants in region of interest in BAM file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - count_roi_variants + Galaxy wrapper id: count_roi_variants + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants + Galaxy wrapper version: 0.0.6 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + - SAM + ToolShed id: count_roi_variants + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: samtools + Conda version: '1.21' + Date of first commit of the suite: '2015-07-29' + Description: BAM coverage statistics using samtools idxstats and depth + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - coverage_stats + Galaxy wrapper id: coverage_stats + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + - SAM + ToolShed id: coverage_stats + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: effectiveT3 + Conda version: 1.0.1 + Date of first commit of the suite: '2015-09-21' + Description: Find bacterial type III effectors in protein sequences + EDAM operation: + - Sequence classification + EDAM operation (no superclasses): + - Sequence classification + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - effectiveT3 + Galaxy wrapper id: effectiveT3 + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 + Galaxy wrapper version: 0.0.21 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://effectors.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: effectivet3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: Prediction of putative Type-III secreted proteins. + bio.tool id: effectivet3 + bio.tool ids: + - effectivet3 + bio.tool name: EffectiveT3 +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2017-02-02' + Description: Filter FASTA sequences by ID (DEPRECATED) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fasta_filter_by_id + Galaxy wrapper id: fasta_filter_by_id + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id + Galaxy wrapper version: 0.0.7 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Fasta Manipulation + - Sequence Analysis + - Text Manipulation + ToolShed id: fasta_filter_by_id + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2017-02-02' + Description: Filter FASTQ sequences by ID (DEPRECATED) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_filter_by_id + Galaxy wrapper id: fastq_filter_by_id + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id + Galaxy wrapper version: 0.0.7 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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fastq_paired_unpaired + Galaxy wrapper id: fastq_paired_unpaired + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired + Galaxy wrapper version: 0.1.5 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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get_orfs_or_cdss + Galaxy wrapper id: get_orfs_or_cdss + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss + Galaxy wrapper version: 0.2.3 + No. of tool users (5 years) (usegalaxy.eu): 746 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1504 + No. of tool users (5 years) - all main servers: 2250 + No. of tool users (all time) (usegalaxy.eu): 746 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1504 + No. of tool users (all time) - all main servers: 2250 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss + Status: To update + Tool usage (5 years) (usegalaxy.eu): 136 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 244 + Tool usage (5 years) - 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mummerplot_wrapper + Galaxy wrapper id: mummer + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer + Galaxy wrapper version: 0.0.8 + No. of tool users (5 years) (usegalaxy.eu): 883 + No. of tool users (5 years) (usegalaxy.org): 730 + No. of tool users (5 years) (usegalaxy.org.au): 136 + No. of tool users (5 years) - all main servers: 1749 + No. of tool users (all time) (usegalaxy.eu): 921 + No. of tool users (all time) (usegalaxy.org): 730 + No. of tool users (all time) (usegalaxy.org.au): 202 + No. of tool users (all time) - all main servers: 1853 + Source: http://mummer.sourceforge.net/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 199 + Tool usage (5 years) (usegalaxy.org): 199 + Tool usage (5 years) (usegalaxy.org.au): 34 + Tool usage (5 years) - all main servers: 432 + Tool usage (all time) (usegalaxy.eu): 211 + Tool usage (all time) (usegalaxy.org): 199 + Tool usage (all time) (usegalaxy.org.au): 49 + Tool usage (all time) - 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predictnls + Galaxy wrapper id: predictnls + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls + Galaxy wrapper version: 0.0.10 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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seq_length + Galaxy wrapper id: seq_length + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length + Galaxy wrapper version: 0.0.5 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Fasta Manipulation + - Fastq Manipulation + - Sequence Analysis + ToolShed id: seq_length + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2015-04-28' + Description: Trim off 5' or 3' primers + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - seq_primer_clip + Galaxy wrapper id: seq_primer_clip + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip + Galaxy wrapper version: 0.0.18 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + - Fasta Manipulation + - Text Manipulation + ToolShed id: seq_primer_clip + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2014-12-02' + Description: Rename sequences with ID mapping from a tabular file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - seq_rename + Galaxy wrapper id: seq_rename + Galaxy wrapper owner: peterjc + Galaxy wrapper parsed folder: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename + Galaxy wrapper source: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename + Galaxy wrapper version: 0.0.10 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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all main servers: 20 + ToolShed categories: + - Assembly + ToolShed id: trimns + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: abricate + Conda version: 1.0.1 + Date of first commit of the suite: '2017-07-10' + Description: Mass screening of contigs for antiobiotic resistance genes + EDAM operation: + - Antimicrobial resistance prediction + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + EDAM topic: + - Genomics + - Microbiology + EDAM topic (no superclasses): + - Genomics + - Microbiology + Galaxy tool ids: + - abricate + - abricate_list + - abricate_summary + Galaxy wrapper id: abricate + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 619817 + No. of tool users (5 years) (usegalaxy.org): 320454 + No. of tool users (5 years) (usegalaxy.org.au): 496156 + No. of tool users (5 years) - all main servers: 1436427 + No. of tool users (all time) (usegalaxy.eu): 622353 + No. of tool users (all time) (usegalaxy.org): 320454 + No. of tool users (all time) (usegalaxy.org.au): 503743 + No. of tool users (all time) - all main servers: 1446550 + Source: https://github.com/tseemann/abricate + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4097 + Tool usage (5 years) (usegalaxy.org): 2915 + Tool usage (5 years) (usegalaxy.org.au): 2012 + Tool usage (5 years) - all main servers: 9024 + Tool usage (all time) (usegalaxy.eu): 4130 + Tool usage (all time) (usegalaxy.org): 2915 + Tool usage (all time) (usegalaxy.org.au): 2227 + Tool usage (all time) - all main servers: 9272 + ToolShed categories: + - Sequence Analysis + ToolShed id: abricate + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 3 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: Mass screening of contigs for antimicrobial resistance or + virulence genes. + bio.tool id: ABRicate + bio.tool ids: + - ABRicate + bio.tool name: ABRicate +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: abritamr + Conda version: 1.0.19 + Date of first commit of the suite: '2023-04-03' + Description: A pipeline for running AMRfinderPlus and collating results into functional + classes + EDAM operation: + - Antimicrobial resistance prediction + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + EDAM topic: + - Microbiology + - Public health and epidemiology + - Infectious disease + EDAM topic (no superclasses): + - Microbiology + - Public health and epidemiology + - Infectious disease + Galaxy tool ids: + - abritamr + Galaxy wrapper id: abritamr + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr + Galaxy wrapper version: 1.0.19 + No. of tool users (5 years) (usegalaxy.eu): 1139 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1139 + No. of tool users (all time) (usegalaxy.eu): 1139 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1139 + Source: https://zenodo.org/record/7370628 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 109 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 109 + Tool usage (all time) (usegalaxy.eu): 109 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 109 + ToolShed categories: + - Sequence Analysis + ToolShed id: abritamr + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: an AMR gene detection pipeline that runs AMRFinderPlus on + a single (or list ) of given isolates and collates the results into a table, separating + genes identified into functionally relevant groups. + bio.tool id: abritamr + bio.tool ids: + - abritamr + bio.tool name: abriTAMR +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: abyss + Conda version: 2.3.9 + Date of first commit of the suite: '2015-04-14' + Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence + assembler + EDAM operation: + - Genome assembly + - De-novo assembly + - Scaffolding + EDAM operation (no superclasses): + - Genome assembly + - De-novo assembly + - Scaffolding + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - abyss-pe + Galaxy wrapper id: abyss + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss + Galaxy wrapper version: 2.3.9 + No. of tool users (5 years) (usegalaxy.eu): 5543 + No. of tool users (5 years) (usegalaxy.org): 1301 + No. of tool users (5 years) (usegalaxy.org.au): 2030 + No. of tool users (5 years) - all main servers: 8874 + No. of tool users (all time) (usegalaxy.eu): 5543 + No. of tool users (all time) (usegalaxy.org): 1305 + No. of tool users (all time) (usegalaxy.org.au): 2030 + No. of tool users (all time) - all main servers: 8878 + Source: http://www.bcgsc.ca/platform/bioinfo/software/abyss + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1042 + Tool usage (5 years) (usegalaxy.org): 413 + Tool usage (5 years) (usegalaxy.org.au): 299 + Tool usage (5 years) - all main servers: 1754 + Tool usage (all time) (usegalaxy.eu): 1042 + Tool usage (all time) (usegalaxy.org): 414 + Tool usage (all time) (usegalaxy.org.au): 299 + Tool usage (all time) - all main servers: 1755 + ToolShed categories: + - Assembly + ToolShed id: abyss + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: De novo genome sequence assembler using short reads. + bio.tool id: abyss + bio.tool ids: + - abyss + bio.tool name: ABySS +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: adapterremoval + Conda version: 2.3.4 + Date of first commit of the suite: '2022-05-04' + Description: Removes residual adapter sequences from single-end (SE) or paired-end + (PE) FASTQ reads. + EDAM operation: + - Sequence trimming + - Sequence merging + - Primer removal + EDAM operation (no superclasses): + - Sequence trimming + - Sequence merging + - Primer removal + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - adapter_removal + Galaxy wrapper id: adapter_removal + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ + Galaxy wrapper version: 2.3.4 + No. of tool users (5 years) (usegalaxy.eu): 348 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 348 + No. of tool users (all time) (usegalaxy.eu): 348 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 348 + Source: https://github.com/MikkelSchubert/adapterremoval + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 62 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 62 + Tool usage (all time) (usegalaxy.eu): 62 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 62 + ToolShed categories: + - Fasta Manipulation + - Sequence Analysis + ToolShed id: adapter_removal + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: AdapterRemoval searches for and removes adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality + bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze + both single end and paired end data, and can be used to merge overlapping paired-ended + reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct + a consensus adapter sequence for paired-ended reads, if which this information + is not available. + bio.tool id: adapterremoval + bio.tool ids: + - adapterremoval + bio.tool name: AdapterRemoval +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2020-03-24' + Description: Add input name as column on an existing tabular file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - addName + Galaxy wrapper id: add_input_name_as_column + Galaxy wrapper owner: mvdbeek + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 76834 + No. of tool users (5 years) (usegalaxy.org): 20174 + No. of tool users (5 years) (usegalaxy.org.au): 11 + No. of tool users (5 years) - all main servers: 97019 + No. of tool users (all time) (usegalaxy.eu): 86002 + No. of tool users (all time) (usegalaxy.org): 20953 + No. of tool users (all time) (usegalaxy.org.au): 11 + No. of tool users (all time) - all main servers: 106966 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column + Status: To update + Tool usage (5 years) (usegalaxy.eu): 227 + Tool usage (5 years) (usegalaxy.org): 312 + Tool usage (5 years) (usegalaxy.org.au): 2 + Tool usage (5 years) - all main servers: 541 + Tool usage (all time) (usegalaxy.eu): 246 + Tool usage (all time) (usegalaxy.org): 395 + Tool usage (all time) (usegalaxy.org.au): 2 + Tool usage (all time) - all main servers: 643 + ToolShed categories: + - Text Manipulation + ToolShed id: add_input_name_as_column + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 4 + Conda id: aegean + Conda version: 0.16.0 + Date of first commit of the suite: '2021-01-03' + Description: AEGeAn toolkit wrappers + EDAM operation: + - Sequence annotation + EDAM operation (no superclasses): + - Sequence annotation + EDAM topic: + - Sequence analysis + - Gene structure + EDAM topic (no superclasses): + - Sequence analysis + - Gene structure + Galaxy tool ids: + - aegean_canongff3 + - aegean_gaeval + - aegean_locuspocus + - aegean_parseval + Galaxy wrapper id: aegean + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean + Galaxy wrapper version: 0.16.0 + No. of tool users (5 years) (usegalaxy.eu): 200 + No. of tool users (5 years) (usegalaxy.org): 83 + No. of tool users (5 years) (usegalaxy.org.au): 1747 + No. of tool users (5 years) - all main servers: 2030 + No. of tool users (all time) (usegalaxy.eu): 200 + No. of tool users (all time) (usegalaxy.org): 83 + No. of tool users (all time) (usegalaxy.org.au): 1747 + No. of tool users (all time) - all main servers: 2030 + Source: https://github.com/BrendelGroup/AEGeAn + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 77 + Tool usage (5 years) (usegalaxy.org): 39 + Tool usage (5 years) (usegalaxy.org.au): 44 + Tool usage (5 years) - all main servers: 160 + Tool usage (all time) (usegalaxy.eu): 77 + Tool usage (all time) (usegalaxy.org): 39 + Tool usage (all time) (usegalaxy.org.au): 44 + Tool usage (all time) - all main servers: 160 + ToolShed categories: + - Transcriptomics + - Sequence Analysis + ToolShed id: aegean + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 4 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 4 + UseGalaxy.or: 4 + biii: null + bio.tool description: Gene Annotation EVAluation. + bio.tool id: gaeval + bio.tool ids: + - gaeval + bio.tool name: GAEVAL +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-aldex2 + Conda version: 1.34.0 + Date of first commit of the suite: '2022-06-29' + Description: Performs analysis Of differential abundance taking sample variation + into account + EDAM operation: + - Statistical inference + EDAM operation (no superclasses): + - Statistical inference + EDAM topic: + - Gene expression + - Statistics and probability + EDAM topic (no superclasses): + - Gene expression + - Statistics and probability + Galaxy tool ids: + - aldex2 + Galaxy wrapper id: aldex2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 + Galaxy wrapper version: 1.26.0 + No. of tool users (5 years) (usegalaxy.eu): 262 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 262 + No. of tool users (all time) (usegalaxy.eu): 262 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 262 + Source: https://github.com/ggloor/ALDEx_bioc + Status: To update + Tool usage (5 years) (usegalaxy.eu): 36 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 36 + Tool usage (all time) (usegalaxy.eu): 36 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 36 + ToolShed categories: + - Metagenomics + ToolShed id: aldex2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: A differential abundance analysis for the comparison of two + or more conditions. It uses a Dirichlet-multinomial model to infer abundance from + counts, that has been optimized for three or more experimental replicates. Infers + sampling variation and calculates the expected FDR given the biological and sampling + variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal + Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg + correction. + bio.tool id: aldex2 + bio.tool ids: + - aldex2 + bio.tool name: ALDEx2 +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: allegro + Conda version: '3' + Date of first commit of the suite: '2017-11-19' + Description: Linkage and haplotype analysis from deCODE + EDAM operation: + - Sequence motif discovery + EDAM operation (no superclasses): + - Sequence motif discovery + EDAM topic: + - Sequence analysis + - Transcription factors and regulatory sites + - DNA + EDAM topic (no superclasses): + - Sequence analysis + - Transcription factors and regulatory sites + - DNA + Galaxy tool ids: + - allegro + Galaxy wrapper id: allegro + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ + Galaxy wrapper version: '@VER@.0' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://www.decode.com/software/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: allegro + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: "It does simultaneous discovery of cis-regulatory motifs and\ + \ their associated expression profiles. Its input are DNA sequences (typically,\ + \ promoters or 3\u2032 UTRs) and genome-wide expression profiles. Its output is\ + \ the set of motifs found, and for each motif the set of genes it regulates (its\ + \ transcriptional module). It is highly efficient and can analyze expression profiles\ + \ of thousands of genes, measured across dozens of experimental conditions, along\ + \ with all regulatory sequences in the genome." + bio.tool id: allegro + bio.tool ids: + - allegro + bio.tool name: Allegro +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-amplican + Conda version: 1.24.0 + Date of first commit of the suite: '2021-09-22' + Description: AmpliCan is an analysis tool for genome editing. + EDAM operation: + - Alignment + - Standardisation and normalisation + EDAM operation (no superclasses): + - Alignment + - Standardisation and normalisation + EDAM topic: + - PCR experiment + - Statistics and probability + EDAM topic (no superclasses): + - PCR experiment + - Statistics and probability + Galaxy tool ids: + - amplican + Galaxy wrapper id: amplican + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican + Galaxy wrapper version: 1.14.0 + No. of tool users (5 years) (usegalaxy.eu): 81 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 81 + No. of tool users (all time) (usegalaxy.eu): 81 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 81 + Source: https://github.com/valenlab/amplican + Status: To update + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 17 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 17 + ToolShed categories: + - Sequence Analysis + ToolShed id: amplican + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: It performs alignment of the amplicon reads, normalizes gathered + data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents + results in form of aggregated reports. Data and statistics can be broken down + by experiments, barcodes, user defined groups, guides and amplicons allowing for + quick identification of potential problems. + bio.tool id: amplican + bio.tool ids: + - amplican + bio.tool name: amplican +- Available on UseGalaxy.eu: 19 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-04-04' + Description: ampvis2 + EDAM operation: + - Analysis + - Visualisation + EDAM operation (no superclasses): + - Analysis + - Visualisation + EDAM topic: + - Biodiversity + EDAM topic (no superclasses): + - Biodiversity + Galaxy tool ids: + - ampvis2_alpha_diversity + - ampvis2_boxplot + - ampvis2_core + - ampvis2_export_fasta + - ampvis2_frequency + - ampvis2_heatmap + - ampvis2_load + - ampvis2_merge_ampvis2 + - ampvis2_mergereplicates + - ampvis2_octave + - ampvis2_ordinate + - ampvis2_otu_network + - ampvis2_rankabundance + - ampvis2_rarecurve + - ampvis2_setmetadata + - ampvis2_subset_samples + - ampvis2_subset_taxa + - ampvis2_timeseries + - ampvis2_venn + Galaxy wrapper id: ampvis2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 + Galaxy wrapper version: 2.8.9 + No. of tool users (5 years) (usegalaxy.eu): 1213 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1213 + No. of tool users (all time) (usegalaxy.eu): 1213 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1213 + Source: https://github.com/MadsAlbertsen/ampvis2/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 155 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 155 + Tool usage (all time) (usegalaxy.eu): 155 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 155 + ToolShed categories: + - Metagenomics + ToolShed id: ampvis2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 19 + Tools available on UseGalaxy.eu: 19 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 19 + UseGalaxy.eu: 19 + biii: null + bio.tool description: ampvis2 is an R-package to conveniently visualise and analyse + 16S rRNA amplicon data in different ways. + bio.tool id: ampvis + bio.tool ids: + - ampvis + bio.tool name: ampvis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: ncbi-amrfinderplus + Conda version: 3.12.8 + Date of first commit of the suite: '2023-05-12' + Description: '"AMRFinderPlus is designed to find acquired antimicrobial resistance + genes and point mutations in protein and/or assembled nucleotide sequences.It + can also search "plus", stress, heat, and biocide resistance and virulence factors + for some organisms.' + EDAM operation: + - Antimicrobial resistance prediction + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + EDAM topic: + - Microbiology + - Public health and epidemiology + - Infectious disease + EDAM topic (no superclasses): + - Microbiology + - Public health and epidemiology + - Infectious disease + Galaxy tool ids: + - amrfinderplus + Galaxy wrapper id: amrfinderplus + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus + Galaxy wrapper version: 3.12.8 + No. of tool users (5 years) (usegalaxy.eu): 5734 + No. of tool users (5 years) (usegalaxy.org): 1035 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6769 + No. of tool users (all time) (usegalaxy.eu): 5734 + No. of tool users (all time) (usegalaxy.org): 1035 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6769 + Source: https://github.com/ncbi/amr + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 334 + Tool usage (5 years) (usegalaxy.org): 106 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 440 + Tool usage (all time) (usegalaxy.eu): 334 + Tool usage (all time) (usegalaxy.org): 106 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 440 + ToolShed categories: + - Sequence Analysis + ToolShed id: AMRFinderPlus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: AMRFinderPlus is designed to find acquired antimicrobial resistance + genes and point mutations in protein and/or assembled nucleotide sequences.It + can also search "plus", stress, heat, and biocide resistance and virulence factors + for some organisms + bio.tool id: amrfinderplus + bio.tool ids: + - amrfinderplus + bio.tool name: AMRFinderPlus +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-ancombc + Conda version: 2.4.0 + Date of first commit of the suite: '2022-07-16' + Description: Performs analysis of compositions of microbiomes with bias correction. + EDAM operation: + - DNA barcoding + EDAM operation (no superclasses): + - DNA barcoding + EDAM topic: + - Microbial ecology + - Metagenomics + - Taxonomy + EDAM topic (no superclasses): + - Microbial ecology + - Metagenomics + - Taxonomy + Galaxy tool ids: + - ancombc + Galaxy wrapper id: ancombc + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc + Galaxy wrapper version: 1.4.0 + No. of tool users (5 years) (usegalaxy.eu): 26 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 26 + No. of tool users (all time) (usegalaxy.eu): 26 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 26 + Source: https://github.com/FrederickHuangLin/ANCOMBC + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - Metagenomics + ToolShed id: ancombc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Determine taxa whose absolute abundances, per unit volume, + of the ecosystem (e.g. gut) are significantly different with changes in the covariate + of interest (e.g. group). The current version of ancombc function implements Analysis + of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional + data while allowing for covariate adjustment. + bio.tool id: ancombc + bio.tool ids: + - ancombc + bio.tool name: ANCOMBC +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: anndata + Conda version: 0.6.22.post1 + Date of first commit of the suite: '2020-10-09' + Description: Import, Export, Inspect and Manipulate Anndata and Loom objects + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - anndata_export + - anndata_import + - anndata_inspect + - anndata_manipulate + - modify_loom + Galaxy wrapper id: anndata + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ + Galaxy wrapper version: 0.10.9 + No. of tool users (5 years) (usegalaxy.eu): 43047 + No. of tool users (5 years) (usegalaxy.org): 17240 + No. of tool users (5 years) (usegalaxy.org.au): 9309 + No. of tool users (5 years) - all main servers: 69596 + No. of tool users (all time) (usegalaxy.eu): 43139 + No. of tool users (all time) (usegalaxy.org): 17240 + No. of tool users (all time) (usegalaxy.org.au): 9309 + No. of tool users (all time) - all main servers: 69688 + Source: https://anndata.readthedocs.io + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1826 + Tool usage (5 years) (usegalaxy.org): 878 + Tool usage (5 years) (usegalaxy.org.au): 298 + Tool usage (5 years) - all main servers: 3002 + Tool usage (all time) (usegalaxy.eu): 1827 + Tool usage (all time) (usegalaxy.org): 878 + Tool usage (all time) (usegalaxy.org.au): 298 + Tool usage (all time) - all main servers: 3003 + ToolShed categories: + - Single Cell + - Spatial Omics + ToolShed id: anndata + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-org.hs.eg.db + Conda version: 3.18.0 + Date of first commit of the suite: '2018-03-11' + Description: 'annotateMyIDs: get annotation for a set of IDs using the Bioconductor + annotation packages' + EDAM operation: + - Annotation + EDAM operation (no superclasses): + - Annotation + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - annotatemyids + Galaxy wrapper id: annotatemyids + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids + Galaxy wrapper version: 3.18.0 + No. of tool users (5 years) (usegalaxy.eu): 29266 + No. of tool users (5 years) (usegalaxy.org): 59299 + No. of tool users (5 years) (usegalaxy.org.au): 5644 + No. of tool users (5 years) - all main servers: 94209 + No. of tool users (all time) (usegalaxy.eu): 30655 + No. of tool users (all time) (usegalaxy.org): 66180 + No. of tool users (all time) (usegalaxy.org.au): 5644 + No. of tool users (all time) - all main servers: 102479 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2849 + Tool usage (5 years) (usegalaxy.org): 5917 + Tool usage (5 years) (usegalaxy.org.au): 1049 + Tool usage (5 years) - all main servers: 9815 + Tool usage (all time) (usegalaxy.eu): 2973 + Tool usage (all time) (usegalaxy.org): 6355 + Tool usage (all time) (usegalaxy.org.au): 1049 + Tool usage (all time) - all main servers: 10377 + ToolShed categories: + - Genome annotation + ToolShed id: annotatemyids + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This tool can get annotation for a generic set of IDs, using + the Bioconductor annotation data packages. Supported organisms are human, mouse, + rat, fruit fly and zebrafish. The org.db packages that are used here are primarily + based on mapping using Entrez Gene identifiers. More information on the annotation + packages can be found at the Bioconductor website, for example, information on + the human annotation package (org.Hs.eg.db) can be found here. + bio.tool id: annotatemyids + bio.tool ids: + - annotatemyids + bio.tool name: annotatemyids +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: argnorm + Conda version: 0.6.0 + Date of first commit of the suite: '2024-08-28' + Description: argNorm is a tool to normalize antibiotic resistance genes (ARGs) by + mapping them to the antibiotic resistance ontology (ARO) created by the CARD database + EDAM operation: + - Gene functional annotation + EDAM operation (no superclasses): + - Gene functional annotation + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - argnorm + Galaxy wrapper id: argnorm + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm + Galaxy wrapper version: 0.6.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/BigDataBiology/argNorm + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Genome annotation + ToolShed id: argnorm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: argNorm is a tool to normalize antibiotic resistance genes + (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by + the CARD database.argNorm also enhances antibiotic resistance gene annotations + by providing drug categorization of the drugs that antibiotic resistance genes + confer resistance to. + bio.tool id: argnorm + bio.tool ids: + - argnorm + bio.tool name: argNorm +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: arriba + Conda version: 2.4.0 + Date of first commit of the suite: '2022-07-27' + Description: Arriba detects fusion genes in RNA-Seq data after running RNA-STAR + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - arriba + - arriba_draw_fusions + - arriba_get_filters + Galaxy wrapper id: arriba + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba + Galaxy wrapper version: 2.4.0 + No. of tool users (5 years) (usegalaxy.eu): 3670 + No. of tool users (5 years) (usegalaxy.org): 3 + No. of tool users (5 years) (usegalaxy.org.au): 234 + No. of tool users (5 years) - all main servers: 3907 + No. of tool users (all time) (usegalaxy.eu): 3670 + No. of tool users (all time) (usegalaxy.org): 3 + No. of tool users (all time) (usegalaxy.org.au): 234 + No. of tool users (all time) - all main servers: 3907 + Source: https://github.com/suhrig/arriba + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 71 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 10 + Tool usage (5 years) - all main servers: 83 + Tool usage (all time) (usegalaxy.eu): 71 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 10 + Tool usage (all time) - all main servers: 83 + ToolShed categories: + - Sequence Analysis + - Transcriptomics + ToolShed id: arriba + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: art + Conda version: 2016.06.05 + Date of first commit of the suite: '2015-04-08' + Description: Simulator for Illumina, 454, and SOLiD sequencing data + EDAM operation: + - Conversion + EDAM operation (no superclasses): + - Conversion + EDAM topic: + - Bioinformatics + EDAM topic (no superclasses): + - Bioinformatics + Galaxy tool ids: + - art_454 + - art_illumina + - art_solid + Galaxy wrapper id: art + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/art + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/art + Galaxy wrapper version: 2014.11.03.0 + No. of tool users (5 years) (usegalaxy.eu): 140 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 140 + No. of tool users (all time) (usegalaxy.eu): 140 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 140 + Source: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Sequence Analysis + - Data Source + ToolShed id: art + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + biii: null + bio.tool description: ART is a set of simulation tools to generate synthetic next-generation + sequencing reads. ART simulates sequencing reads by mimicking real sequencing + process with empirical error models or quality profiles summarized from large + recalibrated sequencing data. ART can also simulate reads using user own read + error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair + reads of three major commercial next-generation sequencing platforms. Illuminas + Solexa, Roches 454 and Applied Biosystems SOLiD + bio.tool id: art + bio.tool ids: + - art + bio.tool name: ART +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 2 + Conda id: artic + Conda version: 1.2.4 + Date of first commit of the suite: '2020-04-22' + Description: 'The artic pipeline is designed to help run the artic bioinformatics + protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: + read filtering, primer trimming, amplicon coverage normalisation,variant calling + and consensus building' + EDAM operation: + - Sequence alignment + EDAM operation (no superclasses): + - Sequence alignment + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - artic_guppyplex + - artic_minion + Galaxy wrapper id: artic + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 9021 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 9021 + No. of tool users (all time) (usegalaxy.eu): 9021 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 9021 + Source: https://github.com/artic-network/fieldbioinformatics + Status: To update + Tool usage (5 years) (usegalaxy.eu): 238 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 238 + Tool usage (all time) (usegalaxy.eu): 238 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 238 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 2 + biii: null + bio.tool description: A bioinformatics pipeline for working with virus sequencing + data sequenced with nanopore + bio.tool id: artic + bio.tool ids: + - artic + bio.tool name: ARTIC +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rjchallis-assembly-stats + Conda version: '17.02' + Date of first commit of the suite: '2023-06-21' + Description: Assembly metric visualisations to facilitate rapid assessment and comparison + of assembly quality. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - assembly_stats + Galaxy wrapper id: assembly-stats + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats + Galaxy wrapper version: '17.02' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/rjchallis/assembly-stats + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + ToolShed id: assembly_stats + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: astral-tree + Conda version: 5.7.8 + Date of first commit of the suite: '2024-08-28' + Description: Tool for estimating an unrooted species tree given a set of unrooted + gene trees + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - astral + Galaxy wrapper id: astral + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral + Galaxy wrapper source: https://github.com/usegalaxy-be/galaxytools/tree/main/astral + Galaxy wrapper version: 5.7.8 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 151 + No. of tool users (5 years) - all main servers: 151 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 151 + No. of tool users (all time) - all main servers: 151 + Source: https://github.com/smirarab/ASTRAL + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 5 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 5 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Phylogenetics + ToolShed id: astral + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: augustus + Conda version: 3.5.0 + Date of first commit of the suite: '2017-10-12' + Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. + EDAM operation: + - Gene prediction + - Ab-initio gene prediction + - Homology-based gene prediction + - Homology-based gene prediction + - Operation + EDAM operation (no superclasses): + - Ab-initio gene prediction + - Homology-based gene prediction + - Homology-based gene prediction + - Operation + EDAM topic: + - Gene transcripts + - Gene and protein families + EDAM topic (no superclasses): + - Gene transcripts + - Gene and protein families + Galaxy tool ids: + - augustus + - augustus_training + Galaxy wrapper id: augustus + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus + Galaxy wrapper version: 3.4.0 + No. of tool users (5 years) (usegalaxy.eu): 12890 + No. of tool users (5 years) (usegalaxy.org): 14901 + No. of tool users (5 years) (usegalaxy.org.au): 6187 + No. of tool users (5 years) - all main servers: 33978 + No. of tool users (all time) (usegalaxy.eu): 13988 + No. of tool users (all time) (usegalaxy.org): 14901 + No. of tool users (all time) (usegalaxy.org.au): 6187 + No. of tool users (all time) - all main servers: 35076 + Source: http://bioinf.uni-greifswald.de/augustus/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1826 + Tool usage (5 years) (usegalaxy.org): 2633 + Tool usage (5 years) (usegalaxy.org.au): 511 + Tool usage (5 years) - all main servers: 4970 + Tool usage (all time) (usegalaxy.eu): 1988 + Tool usage (all time) (usegalaxy.org): 2633 + Tool usage (all time) (usegalaxy.org.au): 511 + Tool usage (all time) - all main servers: 5132 + ToolShed categories: + - Sequence Analysis + ToolShed id: augustus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: AUGUSTUS is a eukaryotic gene prediction tool. It can integrate + evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. + The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment + as input to find new members of the family in a genome. It can be run through + a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. + bio.tool id: augustus + bio.tool ids: + - augustus + bio.tool name: AUGUSTUS +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: b2btools + Conda version: 3.0.7 + Date of first commit of the suite: '2022-08-09' + Description: 'This software suite provides structural predictions for protein sequences + made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational + states, and available experimental data of proteins relate to their amino acid + sequence.Underlying physical and chemical principles are computationally unraveled + through data integration, analysis, and machine learning, so connecting themto + biological events and improving our understanding of the way proteins work.' + EDAM operation: + - Protein disorder prediction + - Protein secondary structure prediction + - Protein feature detection + EDAM operation (no superclasses): + - Protein disorder prediction + - Protein secondary structure prediction + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - b2btools_single_sequence + Galaxy wrapper id: b2btools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools + Galaxy wrapper version: 3.0.5+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 369 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 369 + No. of tool users (all time) (usegalaxy.eu): 369 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 369 + Source: https://bio2byte.be + Status: To update + Tool usage (5 years) (usegalaxy.eu): 19 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 19 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 19 + ToolShed categories: + - Computational chemistry + - Molecular Dynamics + - Proteomics + - Sequence Analysis + - Synthetic Biology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: The bio2byte tools server (b2btools) offers the following + single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- + Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- + Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence + alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein + family as defined in the MSA + bio.tool id: b2btools + bio.tool ids: + - b2btools + bio.tool name: b2bTools +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bakta + Conda version: 1.9.4 + Date of first commit of the suite: '2022-09-01' + Description: '"Bakta is a tool for the rapid & standardized annotation of bacterial + genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including + annotations in machine-readable JSON & bioinformatics standard file formats for + automatic downstream analysis."' + EDAM operation: + - Genome annotation + EDAM operation (no superclasses): + - Genome annotation + EDAM topic: + - Genomics + - Data submission, annotation and curation + - Sequence analysis + EDAM topic (no superclasses): + - Genomics + - Data submission, annotation and curation + - Sequence analysis + Galaxy tool ids: + - bakta + Galaxy wrapper id: bakta + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta + Galaxy wrapper version: 1.9.4 + No. of tool users (5 years) (usegalaxy.eu): 11117 + No. of tool users (5 years) (usegalaxy.org): 19 + No. of tool users (5 years) (usegalaxy.org.au): 9601 + No. of tool users (5 years) - all main servers: 20737 + No. of tool users (all time) (usegalaxy.eu): 11117 + No. of tool users (all time) (usegalaxy.org): 19 + No. of tool users (all time) (usegalaxy.org.au): 9601 + No. of tool users (all time) - all main servers: 20737 + Source: https://github.com/oschwengers/bakta + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 534 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 167 + Tool usage (5 years) - all main servers: 702 + Tool usage (all time) (usegalaxy.eu): 534 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 167 + Tool usage (all time) - all main servers: 702 + ToolShed categories: + - Sequence Analysis + ToolShed id: bakta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Rapid & standardized annotation of bacterial genomes, MAGs + & plasmids + bio.tool id: bakta + bio.tool ids: + - bakta + bio.tool name: Bakta +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: openjdk + Conda version: null + Date of first commit of the suite: '2015-12-07' + Description: Contains a tool that converts a BAM file to an ScIdx file. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bam_to_scidx + Galaxy wrapper id: bam_to_scidx + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 83 + No. of tool users (5 years) (usegalaxy.org): 329 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 412 + No. of tool users (all time) (usegalaxy.eu): 131 + No. of tool users (all time) (usegalaxy.org): 785 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 916 + Source: https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx + Status: To update + Tool usage (5 years) (usegalaxy.eu): 15 + Tool usage (5 years) (usegalaxy.org): 50 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 65 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 210 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 230 + ToolShed categories: + - Convert Formats + ToolShed id: bam_to_scidx + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bamutil + Conda version: 1.0.15 + Date of first commit of the suite: '2021-03-29' + Description: bamUtil is a repository that contains several programs that perform + operations on SAM/BAM files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bamutil_clip_overlap + - bamutil_diff + Galaxy wrapper id: bamutil + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 45 + No. of tool users (5 years) (usegalaxy.org): 69 + No. of tool users (5 years) (usegalaxy.org.au): 258 + No. of tool users (5 years) - all main servers: 372 + No. of tool users (all time) (usegalaxy.eu): 45 + No. of tool users (all time) (usegalaxy.org): 69 + No. of tool users (all time) (usegalaxy.org.au): 258 + No. of tool users (all time) - all main servers: 372 + Source: https://github.com/statgen/bamUtil + Status: To update + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 21 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 42 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 21 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 42 + ToolShed categories: + - Sequence Analysis + ToolShed id: bamutil + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: bandage_ng + Conda version: '2022.09' + Date of first commit of the suite: '2018-09-14' + Description: Bandage - A Bioinformatics Application for Navigating De novo Assembly + Graphs Easily + EDAM operation: + - Sequence assembly visualisation + EDAM operation (no superclasses): + - Sequence assembly visualisation + EDAM topic: + - Genomics + - Sequence assembly + EDAM topic (no superclasses): + - Genomics + - Sequence assembly + Galaxy tool ids: + - bandage_image + - bandage_info + Galaxy wrapper id: bandage + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage + Galaxy wrapper version: '2022.09' + No. of tool users (5 years) (usegalaxy.eu): 55392 + No. of tool users (5 years) (usegalaxy.org): 47603 + No. of tool users (5 years) (usegalaxy.org.au): 18089 + No. of tool users (5 years) - all main servers: 121084 + No. of tool users (all time) (usegalaxy.eu): 56095 + No. of tool users (all time) (usegalaxy.org): 47603 + No. of tool users (all time) (usegalaxy.org.au): 18089 + No. of tool users (all time) - all main servers: 121787 + Source: https://github.com/rrwick/Bandage + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4951 + Tool usage (5 years) (usegalaxy.org): 4916 + Tool usage (5 years) (usegalaxy.org.au): 3121 + Tool usage (5 years) - all main servers: 12988 + Tool usage (all time) (usegalaxy.eu): 5035 + Tool usage (all time) (usegalaxy.org): 4916 + Tool usage (all time) (usegalaxy.org.au): 3121 + Tool usage (all time) - all main servers: 13072 + ToolShed categories: + - Visualization + ToolShed id: bandage + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: GUI program that allows users to interact with the assembly + graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. + It visualises assembly graphs, with connections, using graph layout algorithms. + bio.tool id: bandage + bio.tool ids: + - bandage + bio.tool name: Bandage +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: barcode_splitter + Conda version: 0.18.6 + Date of first commit of the suite: '2019-02-21' + Description: A utility to split sequence files using multiple sets of barcodes + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - barcode_splitter + Galaxy wrapper id: barcode_splitter + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter + Galaxy wrapper version: 0.18.4.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://bitbucket.org/princeton_genomics/barcode_splitter/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Fastq Manipulation + ToolShed id: barcode_splitter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 4 + Conda id: baredsc + Conda version: 1.1.3 + Date of first commit of the suite: '2023-09-06' + Description: baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate + a confidence interval on the probability density function (PDF) of expression + of one or two genes from single-cell RNA-seq data. + EDAM operation: + - Data retrieval + - Expression correlation analysis + - Differential gene expression profiling + EDAM operation (no superclasses): + - Data retrieval + - Expression correlation analysis + - Differential gene expression profiling + EDAM topic: + - RNA-Seq + - Cytometry + - Transcriptomics + - Gene transcripts + - Statistics and probability + EDAM topic (no superclasses): + - RNA-Seq + - Cytometry + - Transcriptomics + - Gene transcripts + - Statistics and probability + Galaxy tool ids: + - baredsc_1d + - baredsc_2d + - baredsc_combine_1d + - baredsc_combine_2d + Galaxy wrapper id: baredsc + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc + Galaxy wrapper version: 1.1.3 + No. of tool users (5 years) (usegalaxy.eu): 111 + No. of tool users (5 years) (usegalaxy.org): 29 + No. of tool users (5 years) (usegalaxy.org.au): 21 + No. of tool users (5 years) - all main servers: 161 + No. of tool users (all time) (usegalaxy.eu): 111 + No. of tool users (all time) (usegalaxy.org): 29 + No. of tool users (all time) (usegalaxy.org.au): 21 + No. of tool users (all time) - all main servers: 161 + Source: https://github.com/lldelisle/baredSC + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 10 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 22 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 10 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 22 + ToolShed categories: + - Single Cell + - Transcriptomics + - Visualization + ToolShed id: baredsc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 4 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.or: 4 + biii: null + bio.tool description: The baredSC (Bayesian Approach to Retreive Expression Distribution + of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence + interval on the probability density function (PDF) of expression of one or two + genes from single-cell RNA-seq data. + bio.tool id: baredsc + bio.tool ids: + - baredsc + bio.tool name: baredSC +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: barrnap + Conda version: '0.9' + Date of first commit of the suite: '2017-08-25' + Description: Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. + EDAM operation: + - Gene prediction + EDAM operation (no superclasses): + - Gene prediction + EDAM topic: + - Genomics + - Model organisms + - Model organisms + EDAM topic (no superclasses): + - Genomics + - Model organisms + - Model organisms + Galaxy tool ids: + - barrnap + Galaxy wrapper id: barrnap + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap + Galaxy wrapper version: 1.2.2 + No. of tool users (5 years) (usegalaxy.eu): 6041 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 6723 + No. of tool users (5 years) - all main servers: 12764 + No. of tool users (all time) (usegalaxy.eu): 6041 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 7273 + No. of tool users (all time) - all main servers: 13314 + Source: https://github.com/tseemann/barrnap + Status: To update + Tool usage (5 years) (usegalaxy.eu): 316 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 240 + Tool usage (5 years) - all main servers: 556 + Tool usage (all time) (usegalaxy.eu): 316 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 322 + Tool usage (all time) - all main servers: 638 + ToolShed categories: + - Sequence Analysis + ToolShed id: barrnap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Predict the location of ribosomal RNA genes in genomes. It + supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) + and eukaryotes (5S,5.8S,28S,18S). + bio.tool id: barrnap + bio.tool ids: + - barrnap + bio.tool name: Barrnap +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: anise_basil + Conda version: 1.2.0 + Date of first commit of the suite: '2019-05-22' + Description: Breakpoint detection, including large insertions + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - basil + Galaxy wrapper id: basil + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil + Galaxy wrapper source: null + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 306 + No. of tool users (5 years) (usegalaxy.org): 467 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 773 + No. of tool users (all time) (usegalaxy.eu): 311 + No. of tool users (all time) (usegalaxy.org): 467 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 778 + Source: https://github.com/seqan/anise_basil + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 82 + Tool usage (5 years) (usegalaxy.org): 99 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 181 + Tool usage (all time) (usegalaxy.eu): 83 + Tool usage (all time) (usegalaxy.org): 99 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 182 + ToolShed categories: + - Variant Analysis + ToolShed id: basil + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bax2bam + Conda version: 0.0.11 + Date of first commit of the suite: '2019-10-12' + Description: BAX to BAM converter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bax2bam + Galaxy wrapper id: bax2bam + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam + Galaxy wrapper version: 0.0.11 + No. of tool users (5 years) (usegalaxy.eu): 208 + No. of tool users (5 years) (usegalaxy.org): 210 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 418 + No. of tool users (all time) (usegalaxy.eu): 208 + No. of tool users (all time) (usegalaxy.org): 210 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 418 + Source: https://github.com/pacificbiosciences/bax2bam/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 26 + Tool usage (5 years) (usegalaxy.org): 30 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 56 + Tool usage (all time) (usegalaxy.eu): 26 + Tool usage (all time) (usegalaxy.org): 30 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 56 + ToolShed categories: + - Convert Formats + - Sequence Analysis + ToolShed id: bax2bam + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bayescan + Conda version: 2.0.1 + Date of first commit of the suite: '2017-03-09' + Description: Detecting natural selection from population-based genetic data + EDAM operation: + - Statistical inference + EDAM operation (no superclasses): + - Statistical inference + EDAM topic: + - Genetics + - Evolutionary biology + - Statistics and probability + - DNA polymorphism + EDAM topic (no superclasses): + - Genetics + - Evolutionary biology + - Statistics and probability + - DNA polymorphism + Galaxy tool ids: + - BayeScan + Galaxy wrapper id: bayescan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ + Galaxy wrapper version: '2.1' + No. of tool users (5 years) (usegalaxy.eu): 90 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 90 + No. of tool users (all time) (usegalaxy.eu): 90 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 90 + Source: http://cmpg.unibe.ch/software/BayeScan/index.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 28 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 28 + Tool usage (all time) (usegalaxy.eu): 28 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 28 + ToolShed categories: + - Sequence Analysis + ToolShed id: bayescan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: BAYEsian genome SCAN for outliers, aims at identifying candidate + loci under natural selection from genetic data, using differences in allele frequencies + between populations. It is based on the multinomial-Dirichlet model. + bio.tool id: bayescan + bio.tool ids: + - bayescan + bio.tool name: BayeScan +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: ucsc-bedgraphtobigwig + Conda version: '469' + Date of first commit of the suite: '2024-06-14' + Description: Make a coverage bigwig from bam, bed or gff, optionally with a chromosome + length file. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - bbgtobigwig + Galaxy wrapper id: bbgbigwig + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig + Galaxy wrapper source: https://www.encodeproject.org/software/bedgraphtobigwig/ + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 42 + No. of tool users (5 years) (usegalaxy.org): 175 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 217 + No. of tool users (all time) (usegalaxy.eu): 42 + No. of tool users (all time) (usegalaxy.org): 175 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 217 + Source: https://www.encodeproject.org/software/bedgraphtobigwig/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 26 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 33 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 26 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 33 + ToolShed categories: + - Convert Formats + ToolShed id: bbgbigwig + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Utilities for handling sequences and assemblies from the UCSC + Genome Browser project. + bio.tool id: UCSC_Genome_Browser_Utilities + bio.tool ids: + - UCSC_Genome_Browser_Utilities + bio.tool name: UCSC Genome Browser Utilities +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 6 + Available on UseGalaxy.org.au: 3 + Conda id: bbmap + Conda version: '39.10' + Date of first commit of the suite: '2021-10-04' + Description: BBTools is a suite of fast, multithreaded bioinformatics tools designed + for analysis of DNA and RNA sequence data.BBTools can handle common sequencing + file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with + autodetection of quality encoding and interleaving. It is written in Java and + works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows + and Linux; there are no dependencies other than Java (version7 or higher). Program + descriptions and options are shown when running the shell scripts with no parameters. + EDAM operation: + - RNA-Seq analysis + - Sequence trimming + - Read mapping + - Sequence contamination filtering + - Read binning + - Sequence alignment + EDAM operation (no superclasses): + - RNA-Seq analysis + - Sequence trimming + - Read mapping + - Sequence contamination filtering + - Read binning + - Sequence alignment + EDAM topic: + - Sequencing + - RNA splicing + - Whole genome sequencing + - Phylogenetics + - Metagenomics + - RNA-Seq + EDAM topic (no superclasses): + - RNA splicing + - Whole genome sequencing + - Phylogenetics + - Metagenomics + - RNA-Seq + Galaxy tool ids: + - bbtools_bbduk + - bbtools_bbmap + - bbtools_bbmerge + - bbtools_bbnorm + - bbtools_callvariants + - bbtools_tadpole + Galaxy wrapper id: bbtools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools + Galaxy wrapper version: '39.08' + No. of tool users (5 years) (usegalaxy.eu): 11989 + No. of tool users (5 years) (usegalaxy.org): 4458 + No. of tool users (5 years) (usegalaxy.org.au): 2507 + No. of tool users (5 years) - all main servers: 18954 + No. of tool users (all time) (usegalaxy.eu): 11989 + No. of tool users (all time) (usegalaxy.org): 4458 + No. of tool users (all time) (usegalaxy.org.au): 2507 + No. of tool users (all time) - all main servers: 18954 + Source: https://jgi.doe.gov/data-and-tools/bbtools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 768 + Tool usage (5 years) (usegalaxy.org): 652 + Tool usage (5 years) (usegalaxy.org.au): 80 + Tool usage (5 years) - all main servers: 1500 + Tool usage (all time) (usegalaxy.eu): 768 + Tool usage (all time) (usegalaxy.org): 652 + Tool usage (all time) (usegalaxy.org.au): 80 + Tool usage (all time) - all main servers: 1500 + ToolShed categories: + - Sequence Analysis + ToolShed id: bbtools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 6 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 5 + UseGalaxy.fr: 1 + UseGalaxy.or: 3 + biii: null + bio.tool description: BBMap is a fast splice-aware aligner for RNA and DNA. It + is faster than almost all short-read aligners, yet retains unrivaled sensitivity + and specificity, particularly for reads with many errors and indels. + bio.tool id: bbmap + bio.tool ids: + - bbmap + - bbtools + bio.tool name: BBMap +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bcftools + Conda version: '1.21' + Date of first commit of the suite: '2021-01-03' + Description: BCFtools toolkit wrappers + EDAM operation: + - Data handling + - Variant calling + EDAM operation (no superclasses): + - Data handling + - Variant calling + EDAM topic: + - Genetic variation + - DNA polymorphism + - GWAS study + - Genotyping experiment + EDAM topic (no superclasses): + - DNA polymorphism + - GWAS study + - Genotyping experiment + Galaxy tool ids: + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@_from_vcf + - bcftools_@EXECUTABLE@_to_vcf + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_plugin_@PLUGIN_ID@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@_list_samples + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + - bcftools_@EXECUTABLE@ + Galaxy wrapper id: bcftools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools + Galaxy wrapper version: 1.15.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://samtools.github.io/bcftools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: BCFtools is a set of utilities that manipulate variant calls + in the Variant Call Format (VCF) and its binary counterpart BCF. All commands + work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. + bio.tool id: bcftools + bio.tool ids: + - bcftools + bio.tool name: BCFtools +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bctools + Conda version: 0.2.2 + Date of first commit of the suite: '2017-10-09' + Description: 'bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools + can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to + extract barcodes from arbitrary positions relative to the read starts,to clean + up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes + as used with uvCLAP and FLASH.License: Apache License 2.0' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bctools_convert_to_binary_barcode + - bctools_extract_crosslinked_nucleotides + - bctools_extract_alignment_ends + - bctools_extract_barcodes + - bctools_merge_pcr_duplicates + - bctools_remove_tail + - bctools_remove_spurious_events + Galaxy wrapper id: bctools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools + Galaxy wrapper version: 0.2.2 + No. of tool users (5 years) (usegalaxy.eu): 2352 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2352 + No. of tool users (all time) (usegalaxy.eu): 3092 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3092 + Source: https://github.com/dmaticzka/bctools + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 234 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 234 + Tool usage (all time) (usegalaxy.eu): 265 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 265 + ToolShed categories: + - Sequence Analysis + - Transcriptomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 7 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + UseGalaxy.no: 7 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 12 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: beacon2-import + Conda version: 2.2.4 + Date of first commit of the suite: '2024-07-22' + Description: Beacon Import uploads local genetic data to the server, while Beacon + Query searches for genetic information such as genes, sequences, and variants. + EDAM operation: + - Service discovery + - Database search + - Genetic variation analysis + EDAM operation (no superclasses): + - Service discovery + - Database search + - Genetic variation analysis + EDAM topic: + - Genetic variation + - Population genetics + - Data security + - Rare diseases + EDAM topic (no superclasses): + - Genetic variation + - Population genetics + - Data security + - Rare diseases + Galaxy tool ids: + - beacon2_analyses + - beacon2_biosamples + - beacon2_bracket + - beacon2_cnv + - beacon2_cohorts + - beacon2_datasets + - beacon2_gene + - beacon2_import + - beacon2_individuals + - beacon2_range + - beacon2_runs + - beacon2_sequence + Galaxy wrapper id: beacon2-import + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import + Galaxy wrapper version: 2.2.4 + No. of tool users (5 years) (usegalaxy.eu): 22 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 22 + No. of tool users (all time) (usegalaxy.eu): 22 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 22 + Source: https://pypi.org/project/beacon2-import/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - Variant Analysis + ToolShed id: Beacon2_Import + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 12 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 12 + biii: null + bio.tool description: A global search engine for genetic mutations. + bio.tool id: ga4gh_beacon + bio.tool ids: + - ga4gh_beacon + bio.tool name: GA4GH Beacon +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: beacon2-ri-tools + Conda version: 2.0.0 + Date of first commit of the suite: '2023-08-17' + Description: beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation + (B2RI). + EDAM operation: + - Service discovery + - Database search + - Genetic variation analysis + EDAM operation (no superclasses): + - Service discovery + - Database search + - Genetic variation analysis + EDAM topic: + - Genetic variation + - Population genetics + - Data security + - Rare diseases + EDAM topic (no superclasses): + - Genetic variation + - Population genetics + - Data security + - Rare diseases + Galaxy tool ids: + - beacon2_csv2xlsx + - beacon2_pxf2bff + - beacon2_vcf2bff + Galaxy wrapper id: beacon2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 + Galaxy wrapper version: 2.0.0 + No. of tool users (5 years) (usegalaxy.eu): 33 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 33 + No. of tool users (all time) (usegalaxy.eu): 33 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 33 + Source: https://github.com/EGA-archive/beacon2-ri-tools/tree/main + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Variant Analysis + ToolShed id: beacon2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + biii: null + bio.tool description: A global search engine for genetic mutations. + bio.tool id: ga4gh_beacon + bio.tool ids: + - ga4gh_beacon + bio.tool name: GA4GH Beacon +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: beagle + Conda version: 5.4_22Jul22.46e + Date of first commit of the suite: '2021-07-03' + Description: Beagle is a program for phasing and imputing missing genotypes. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - beagle + Galaxy wrapper id: beagle + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle + Galaxy wrapper version: 5.2_21Apr21.304 + No. of tool users (5 years) (usegalaxy.eu): 88 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 88 + No. of tool users (all time) (usegalaxy.eu): 88 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 88 + Source: https://faculty.washington.edu/browning/beagle/beagle.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 28 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 28 + Tool usage (all time) (usegalaxy.eu): 28 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 28 + ToolShed categories: + - Variant Analysis + ToolShed id: beagle + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bedops + Conda version: 2.4.41 + Date of first commit of the suite: '2023-08-08' + Description: 'BEDOPS: high-performance genomic feature operations' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bedops-sort-bed + Galaxy wrapper id: bedops + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops + Galaxy wrapper source: https://bedops.readthedocs.io/ + Galaxy wrapper version: 2.4.41 + No. of tool users (5 years) (usegalaxy.eu): 93 + No. of tool users (5 years) (usegalaxy.org): 181 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 274 + No. of tool users (all time) (usegalaxy.eu): 93 + No. of tool users (all time) (usegalaxy.org): 181 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 274 + Source: https://bedops.readthedocs.io/en/latest/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 36 + Tool usage (5 years) (usegalaxy.org): 62 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 98 + Tool usage (all time) (usegalaxy.eu): 36 + Tool usage (all time) (usegalaxy.org): 62 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 98 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: bedops_sortbed + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 37 + Available on UseGalaxy.fr: 37 + Available on UseGalaxy.org (Main): 37 + Available on UseGalaxy.org.au: 37 + Conda id: bedtools + Conda version: 2.31.1 + Date of first commit of the suite: '2019-09-05' + Description: bedtools is a powerful toolset for genome arithmetic + EDAM operation: + - Mapping + EDAM operation (no superclasses): + - Mapping + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - bedtools_annotatebed + - bedtools_bamtobed + - bedtools_bed12tobed6 + - bedtools_bedtobam + - bedtools_bedtoigv + - bedtools_bedpetobam + - bedtools_closestbed + - bedtools_clusterbed + - bedtools_complementbed + - bedtools_coveragebed + - bedtools_expandbed + - bedtools_fisher + - bedtools_flankbed + - bedtools_genomecoveragebed + - bedtools_getfastabed + - bedtools_groupbybed + - bedtools_intersectbed + - bedtools_jaccard + - bedtools_links + - bedtools_makewindowsbed + - bedtools_map + - bedtools_maskfastabed + - bedtools_mergebed + - bedtools_multicovtbed + - bedtools_multiintersectbed + - bedtools_nucbed + - bedtools_overlapbed + - bedtools_randombed + - bedtools_reldistbed + - bedtools_shufflebed + - bedtools_slopbed + - bedtools_sortbed + - bedtools_spacingbed + - bedtools_subtractbed + - bedtools_tagbed + - bedtools_unionbedgraph + - bedtools_windowbed + Galaxy wrapper id: bedtools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools + Galaxy wrapper version: 2.31.1 + No. of tool users (5 years) (usegalaxy.eu): 916111 + No. of tool users (5 years) (usegalaxy.org): 407944 + No. of tool users (5 years) (usegalaxy.org.au): 84008 + No. of tool users (5 years) - all main servers: 1408063 + No. of tool users (all time) (usegalaxy.eu): 962278 + No. of tool users (all time) (usegalaxy.org): 647621 + No. of tool users (all time) (usegalaxy.org.au): 89233 + No. of tool users (all time) - all main servers: 1699132 + Source: https://github.com/arq5x/bedtools2 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 13235 + Tool usage (5 years) (usegalaxy.org): 25849 + Tool usage (5 years) (usegalaxy.org.au): 2486 + Tool usage (5 years) - all main servers: 41570 + Tool usage (all time) (usegalaxy.eu): 14525 + Tool usage (all time) (usegalaxy.org): 41751 + Tool usage (all time) (usegalaxy.org.au): 2832 + Tool usage (all time) - all main servers: 59108 + ToolShed categories: + - Genomic Interval Operations + - Text Manipulation + ToolShed id: bedtools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 37 + Tools available on Galaxy@Pasteur: 6 + Tools available on GalaxyTrakr: 37 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 37 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 37 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 37 + Tools available on UseGalaxy.cz: 37 + Tools available on UseGalaxy.eu: 37 + Tools available on UseGalaxy.fr: 37 + Tools available on UseGalaxy.no: 37 + Tools available on UseGalaxy.org (Main): 37 + Tools available on UseGalaxy.org.au: 37 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 37 + UseGalaxy.cz: 37 + UseGalaxy.eu: 37 + UseGalaxy.fr: 37 + UseGalaxy.no: 37 + UseGalaxy.or: 37 + biii: null + bio.tool description: BEDTools is an extensive suite of utilities for comparing + genomic features in BED format. + bio.tool id: bedtools + bio.tool ids: + - bedtools + bio.tool name: BEDTools +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bellerophon + Conda version: '1.0' + Date of first commit of the suite: '2021-05-28' + Description: Filter mapped reads where the mapping spans a junction, retaining the + 5-prime read. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bellerophon + Galaxy wrapper id: bellerophon + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon + Galaxy wrapper source: https://github.com/davebx/bellerophon + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 1611 + No. of tool users (5 years) (usegalaxy.org): 763 + No. of tool users (5 years) (usegalaxy.org.au): 543 + No. of tool users (5 years) - all main servers: 2917 + No. of tool users (all time) (usegalaxy.eu): 1611 + No. of tool users (all time) (usegalaxy.org): 763 + No. of tool users (all time) (usegalaxy.org.au): 543 + No. of tool users (all time) - all main servers: 2917 + Source: https://github.com/davebx/bellerophon + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 262 + Tool usage (5 years) (usegalaxy.org): 67 + Tool usage (5 years) (usegalaxy.org.au): 30 + Tool usage (5 years) - all main servers: 359 + Tool usage (all time) (usegalaxy.eu): 262 + Tool usage (all time) (usegalaxy.org): 67 + Tool usage (all time) (usegalaxy.org.au): 30 + Tool usage (all time) - all main servers: 359 + ToolShed categories: + - Sequence Analysis + ToolShed id: bellerophon + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: berokka + Conda version: 0.2.3 + Date of first commit of the suite: '2019-03-08' + Description: Berokka is used to trim, circularise, orient & filter long read bacterial + genome assemblies. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - berokka + Galaxy wrapper id: berokka + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka + Galaxy wrapper version: 0.2.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 617 + No. of tool users (5 years) - all main servers: 617 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 617 + No. of tool users (all time) - all main servers: 617 + Source: https://github.com/tseemann/berokka + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 63 + Tool usage (5 years) - all main servers: 63 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 63 + Tool usage (all time) - all main servers: 63 + ToolShed categories: + - Fasta Manipulation + ToolShed id: berokka + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bigscape + Conda version: 1.1.9 + Date of first commit of the suite: '2024-02-18' + Description: Construct sequence similarity networks of BGCs and groups them into + GCF + EDAM operation: + - Clustering + - Global alignment + - Fold recognition + EDAM operation (no superclasses): + - Clustering + - Global alignment + - Fold recognition + EDAM topic: + - Phylogeny + - Microbial ecology + - Mapping + - Metabolomics + - Bioinformatics + - Gene and protein families + EDAM topic (no superclasses): + - Phylogeny + - Microbial ecology + - Mapping + - Metabolomics + - Bioinformatics + - Gene and protein families + Galaxy tool ids: + - bigscape + Galaxy wrapper id: bigscape + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ + Galaxy wrapper version: 1.1.9 + No. of tool users (5 years) (usegalaxy.eu): 544 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 544 + No. of tool users (all time) (usegalaxy.eu): 544 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 544 + Source: https://github.com/medema-group/BiG-SCAPE + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 20 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 20 + ToolShed categories: + - Metagenomics + ToolShed id: bigscape + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: A computational framework to explore large-scale biosynthetic + diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) + is a software package, written in Python, that constructs sequence similarity + networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster + Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix + between gene clusters based on a comparison of their protein domain content, order, + copy number and sequence identity.It defines a distance metric between Gene Clusters + using a combination of three indices (Jaccard Index of domain types, Domain Sequence + Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore + the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, + by constructing BGC sequence similarity networks, grouping BGCs into gene cluster + families, and exploring gene cluster diversity linked to enzyme phylogenies. + bio.tool id: BiG-SCAPE + bio.tool ids: + - BiG-SCAPE + bio.tool name: BiG-SCAPE +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2024-07-05' + Description: pybigtools and numpy code to find continuous runs above a high or below + a low quantile cutpoint in bigwig files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bigwig_outlier_bed + Galaxy wrapper id: bigwig_outlier_bed + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 218 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 218 + No. of tool users (all time) (usegalaxy.eu): 218 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 218 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Sequence Analysis + ToolShed id: bigwig_outlier_bed + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Bigtools is a library and associated tools for reading and + writing bigwig and bigbed files. Rust. + bio.tool id: bigtools + bio.tool ids: + - bigtools + bio.tool name: bigtools +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: binning_refiner + Conda version: 1.4.3 + Date of first commit of the suite: '2022-02-18' + Description: Reconciles the outputs of different binning programs with the aim to + improve the quality of genome bins,especially with respect to contamination levels. + EDAM operation: + - Read binning + - Sequence clustering + EDAM operation (no superclasses): + - Read binning + - Sequence clustering + EDAM topic: + - Metagenomics + - Sequence assembly + - Microbial ecology + EDAM topic (no superclasses): + - Metagenomics + - Sequence assembly + - Microbial ecology + Galaxy tool ids: + - bin_refiner + Galaxy wrapper id: binning_refiner + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ + Galaxy wrapper version: 1.4.3 + No. of tool users (5 years) (usegalaxy.eu): 126 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 126 + No. of tool users (all time) (usegalaxy.eu): 126 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 126 + Source: https://github.com/songweizhi/Binning_refiner + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 42 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 42 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 42 + ToolShed categories: + - Metagenomics + ToolShed id: binning_refiner + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Improving genome bins through the combination of different + binning programs + bio.tool id: binning_refiner + bio.tool ids: + - binning_refiner + bio.tool name: Binning_refiner +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: python-bioext + Conda version: 0.21.9 + Date of first commit of the suite: '2018-04-23' + Description: A suite of Galaxy tools designed around the BioExt extension to BioPython. + Align sequences, merge duplicate sequences into one, and more! + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bioext_bam2msa + - bioext_bealign + Galaxy wrapper id: bioext + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext + Galaxy wrapper source: https://github.com/davebx/bioext-gx/ + Galaxy wrapper version: 0.21.9 + No. of tool users (5 years) (usegalaxy.eu): 17413 + No. of tool users (5 years) (usegalaxy.org): 15349 + No. of tool users (5 years) (usegalaxy.org.au): 2 + No. of tool users (5 years) - all main servers: 32764 + No. of tool users (all time) (usegalaxy.eu): 17413 + No. of tool users (all time) (usegalaxy.org): 15349 + No. of tool users (all time) (usegalaxy.org.au): 2 + No. of tool users (all time) - all main servers: 32764 + Source: https://pypi.python.org/pypi/biopython-extensions/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 822 + Tool usage (5 years) (usegalaxy.org): 2020 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 2843 + Tool usage (all time) (usegalaxy.eu): 822 + Tool usage (all time) (usegalaxy.org): 2020 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 2843 + ToolShed categories: + - Next Gen Mappers + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2023-01-25' + Description: Miscellanea of scripts for bioinformatics + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fasta_regex_finder + Galaxy wrapper id: bioinformatics_cafe + Galaxy wrapper owner: mbernt + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 1137 + No. of tool users (5 years) (usegalaxy.org): 1029 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2166 + No. of tool users (all time) (usegalaxy.eu): 1137 + No. of tool users (all time) (usegalaxy.org): 1029 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2166 + Source: https://github.com/dariober/bioinformatics-cafe/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 97 + Tool usage (5 years) (usegalaxy.org): 71 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 168 + Tool usage (all time) (usegalaxy.eu): 97 + Tool usage (all time) (usegalaxy.org): 71 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 168 + ToolShed categories: + - Sequence Analysis + ToolShed id: bioinformatics_cafe + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: biom-format + Conda version: 2.1.7 + Date of first commit of the suite: '2016-06-07' + Description: The biom-format package provides a command line interface and Python + API for working with BIOM files. + EDAM operation: + - Formatting + EDAM operation (no superclasses): + - Formatting + EDAM topic: + - Laboratory information management + - Sequence analysis + EDAM topic (no superclasses): + - Laboratory information management + - Sequence analysis + Galaxy tool ids: + - biom_add_metadata + - biom_convert + - biom_from_uc + - biom_normalize_table + - biom_subset_table + - biom_summarize_table + Galaxy wrapper id: biom_format + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format + Galaxy wrapper version: 2.1.15 + No. of tool users (5 years) (usegalaxy.eu): 12725 + No. of tool users (5 years) (usegalaxy.org): 2851 + No. of tool users (5 years) (usegalaxy.org.au): 2171 + No. of tool users (5 years) - all main servers: 17747 + No. of tool users (all time) (usegalaxy.eu): 12725 + No. of tool users (all time) (usegalaxy.org): 5049 + No. of tool users (all time) (usegalaxy.org.au): 2371 + No. of tool users (all time) - all main servers: 20145 + Source: https://github.com/biocore/biom-format + Status: To update + Tool usage (5 years) (usegalaxy.eu): 297 + Tool usage (5 years) (usegalaxy.org): 450 + Tool usage (5 years) (usegalaxy.org.au): 214 + Tool usage (5 years) - all main servers: 961 + Tool usage (all time) (usegalaxy.eu): 297 + Tool usage (all time) (usegalaxy.org): 638 + Tool usage (all time) (usegalaxy.org.au): 239 + Tool usage (all time) - all main servers: 1174 + ToolShed categories: + - Metagenomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 6 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 2 + biii: null + bio.tool description: This package includes basic tools for reading biom-format + files, accessing and subsetting data tables from a biom object, as well as limited + support for writing a biom-object back to a biom-format file. The design of this + API is intended to match the python API and other tools included with the biom-format + project, but with a decidedly "R flavor" that should be familiar to R users. This + includes S4 classes and methods, as well as extensions of common core functions/methods. + bio.tool id: biomformat + bio.tool ids: + - biomformat + bio.tool name: biomformat +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: perl-bioperl + Conda version: 1.7.8 + Date of first commit of the suite: '2015-08-14' + Description: Converts GenBank format files to GFF3 + EDAM operation: + - Data handling + - Service invocation + EDAM operation (no superclasses): + - Data handling + - Service invocation + EDAM topic: + - Genomics + - Software engineering + - Data management + EDAM topic (no superclasses): + - Genomics + - Software engineering + Galaxy tool ids: + - bp_genbank2gff3 + Galaxy wrapper id: bioperl + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 7738 + No. of tool users (5 years) (usegalaxy.org): 8301 + No. of tool users (5 years) (usegalaxy.org.au): 1369 + No. of tool users (5 years) - all main servers: 17408 + No. of tool users (all time) (usegalaxy.eu): 7931 + No. of tool users (all time) (usegalaxy.org): 8301 + No. of tool users (all time) (usegalaxy.org.au): 1369 + No. of tool users (all time) - all main servers: 17601 + Source: https://bioperl.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 478 + Tool usage (5 years) (usegalaxy.org): 849 + Tool usage (5 years) (usegalaxy.org.au): 154 + Tool usage (5 years) - all main servers: 1481 + Tool usage (all time) (usegalaxy.eu): 508 + Tool usage (all time) (usegalaxy.org): 849 + Tool usage (all time) (usegalaxy.org.au): 154 + Tool usage (all time) - all main servers: 1511 + ToolShed categories: + - Sequence Analysis + ToolShed id: bp_genbank2gff3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A collection of Perl modules that facilitate the development + of Perl scripts for bioinformatics applications. It provides software modules + for many of the typical tasks of bioinformatics programming. + bio.tool id: bioperl + bio.tool ids: + - bioperl + bio.tool name: BioPerl +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: biscot + Conda version: 2.3.3 + Date of first commit of the suite: '2023-01-06' + Description: Bionano scaffolding correction tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - biscot + Galaxy wrapper id: biscot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot + Galaxy wrapper source: https://github.com/bgruening/iuc/tree/master/tools/biscot + Galaxy wrapper version: 2.3.3 + No. of tool users (5 years) (usegalaxy.eu): 3 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3 + No. of tool users (all time) (usegalaxy.eu): 3 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3 + Source: https://github.com/institut-de-genomique/biscot + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Assembly + ToolShed id: biscot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: magicblast + Conda version: 1.7.0 + Date of first commit of the suite: '2022-04-05' + Description: Maps large next-generation RNA or DNA sequencing runs against a whole + genome or transcriptome + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - magicblast + Galaxy wrapper id: blast + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast + Galaxy wrapper version: 1.7.0 + No. of tool users (5 years) (usegalaxy.eu): 738 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 2 + No. of tool users (5 years) - all main servers: 740 + No. of tool users (all time) (usegalaxy.eu): 738 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 2 + No. of tool users (all time) - all main servers: 740 + Source: https://ncbi.github.io/magicblast/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 151 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 152 + Tool usage (all time) (usegalaxy.eu): 151 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 152 + ToolShed categories: + - Next Gen Mappers + ToolShed id: magicblast + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bcbiogff + Conda version: 0.6.6 + Date of first commit of the suite: '2015-05-25' + Description: BlastXML to gapped GFF3 + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - blastxml_to_gapped_gff3 + Galaxy wrapper id: blastxml_to_gapped_gff3 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 585 + No. of tool users (5 years) (usegalaxy.org): 172 + No. of tool users (5 years) (usegalaxy.org.au): 135 + No. of tool users (5 years) - all main servers: 892 + No. of tool users (all time) (usegalaxy.eu): 585 + No. of tool users (all time) (usegalaxy.org): 172 + No. of tool users (all time) (usegalaxy.org.au): 135 + No. of tool users (all time) - all main servers: 892 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 102 + Tool usage (5 years) (usegalaxy.org): 63 + Tool usage (5 years) (usegalaxy.org.au): 16 + Tool usage (5 years) - all main servers: 181 + Tool usage (all time) (usegalaxy.eu): 102 + Tool usage (all time) (usegalaxy.org): 63 + Tool usage (all time) (usegalaxy.org.au): 16 + Tool usage (all time) - all main servers: 181 + ToolShed categories: + - Convert Formats + - Sequence Analysis + ToolShed id: blastxml_to_gapped_gff3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bowtie2 + Conda version: 2.5.4 + Date of first commit of the suite: '2018-04-10' + Description: 'Bowtie2: Fast and sensitive read alignment' + EDAM operation: + - Read mapping + EDAM operation (no superclasses): + - Read mapping + EDAM topic: + - Mapping + - Genomics + - Mapping + EDAM topic (no superclasses): + - Mapping + - Genomics + - Mapping + Galaxy tool ids: + - bowtie2 + Galaxy wrapper id: bowtie2 + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 + Galaxy wrapper version: 2.5.3 + No. of tool users (5 years) (usegalaxy.eu): 397893 + No. of tool users (5 years) (usegalaxy.org): 577209 + No. of tool users (5 years) (usegalaxy.org.au): 60105 + No. of tool users (5 years) - all main servers: 1035207 + No. of tool users (all time) (usegalaxy.eu): 427447 + No. of tool users (all time) (usegalaxy.org): 903193 + No. of tool users (all time) (usegalaxy.org.au): 67495 + No. of tool users (all time) - all main servers: 1398135 + Source: http://bowtie-bio.sourceforge.net/bowtie2 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 12133 + Tool usage (5 years) (usegalaxy.org): 33086 + Tool usage (5 years) (usegalaxy.org.au): 3779 + Tool usage (5 years) - all main servers: 48998 + Tool usage (all time) (usegalaxy.eu): 13176 + Tool usage (all time) (usegalaxy.org): 52020 + Tool usage (all time) (usegalaxy.org.au): 4271 + Tool usage (all time) - all main servers: 69467 + ToolShed categories: + - Next Gen Mappers + ToolShed id: bowtie2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 1 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. It is particularly good at aligning + reads of about 50 up to 100s or 1,000s of characters, and particularly good at + aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome + with an FM Index to keep its memory footprint small: for the human genome, its + memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, + and paired-end alignment modes.' + bio.tool id: bowtie2 + bio.tool ids: + - bowtie2 + bio.tool name: Bowtie 2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bracken + Conda version: '3.0' + Date of first commit of the suite: '2019-10-15' + Description: Bayesian Reestimation of Abundance with KrakEN + EDAM operation: + - Statistical calculation + EDAM operation (no superclasses): + - Statistical calculation + EDAM topic: + - Metagenomics + - Microbial ecology + EDAM topic (no superclasses): + - Metagenomics + - Microbial ecology + Galaxy tool ids: + - est_abundance + Galaxy wrapper id: bracken + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken + Galaxy wrapper version: '3.0' + No. of tool users (5 years) (usegalaxy.eu): 51378 + No. of tool users (5 years) (usegalaxy.org): 3298 + No. of tool users (5 years) (usegalaxy.org.au): 1660 + No. of tool users (5 years) - all main servers: 56336 + No. of tool users (all time) (usegalaxy.eu): 51378 + No. of tool users (all time) (usegalaxy.org): 3298 + No. of tool users (all time) (usegalaxy.org.au): 1660 + No. of tool users (all time) - all main servers: 56336 + Source: https://ccb.jhu.edu/software/bracken/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 775 + Tool usage (5 years) (usegalaxy.org): 160 + Tool usage (5 years) (usegalaxy.org.au): 63 + Tool usage (5 years) - all main servers: 998 + Tool usage (all time) (usegalaxy.eu): 775 + Tool usage (all time) (usegalaxy.org): 160 + Tool usage (all time) (usegalaxy.org.au): 63 + Tool usage (all time) - all main servers: 998 + ToolShed categories: + - Sequence Analysis + - Metagenomics + ToolShed id: bracken + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Statistical method that computes the abundance of species + in DNA sequences from a metagenomics sample. + bio.tool id: bracken + bio.tool ids: + - bracken + bio.tool name: Bracken +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: breseq + Conda version: 0.39.0 + Date of first commit of the suite: '2019-10-21' + Description: Predicts mutations in microbial genomes + EDAM operation: + - Polymorphism detection + EDAM operation (no superclasses): + - Polymorphism detection + EDAM topic: + - Sequencing + - Sequence analysis + - DNA mutation + EDAM topic (no superclasses): + - Sequencing + - Sequence analysis + - DNA mutation + Galaxy tool ids: + - breseq + Galaxy wrapper id: breseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq + Galaxy wrapper source: null + Galaxy wrapper version: 0.35.5 + No. of tool users (5 years) (usegalaxy.eu): 2976 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 884 + No. of tool users (5 years) - all main servers: 3860 + No. of tool users (all time) (usegalaxy.eu): 2976 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 884 + No. of tool users (all time) - all main servers: 3860 + Source: https://github.com/barricklab/breseq + Status: To update + Tool usage (5 years) (usegalaxy.eu): 98 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 70 + Tool usage (5 years) - all main servers: 168 + Tool usage (all time) (usegalaxy.eu): 98 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 70 + Tool usage (all time) - all main servers: 168 + ToolShed categories: + - Variant Analysis + ToolShed id: breseq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Runs Breseq software on a set of fastq files. + bio.tool id: breseq + bio.tool ids: + - breseq + bio.tool name: breseq +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-06-11' + Description: Extend 3' end of a GTF using another GTF as a template + EDAM operation: + - Genome annotation + EDAM operation (no superclasses): + - Genome annotation + EDAM topic: + - Transcriptomics + - Genomics + EDAM topic (no superclasses): + - Transcriptomics + Galaxy tool ids: + - brew3r_r + Galaxy wrapper id: brew3r_r + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 6 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 6 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7 + Source: https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 3 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Transcriptomics + - RNA + ToolShed id: brew3r_r + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This R package provide functions that are used in the BREW3R + workflow. This mainly contains a function that extend a gtf as GRanges using information + from another gtf (also as GRanges). The process allows to extend gene annotation + without increasing the overlap between gene ids. + bio.tool id: brew3r.r + bio.tool ids: + - brew3r.r + bio.tool name: BREW3R.r +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: busco + Conda version: 5.8.0 + Date of first commit of the suite: '2019-12-01' + Description: BUSCO assess genome and annotation completeness + EDAM operation: + - Sequence assembly validation + - Scaffolding + - Genome assembly + - Transcriptome assembly + EDAM operation (no superclasses): + - Sequence assembly validation + - Scaffolding + - Genome assembly + - Transcriptome assembly + EDAM topic: + - Sequence assembly + - Genomics + - Transcriptomics + - Sequence analysis + EDAM topic (no superclasses): + - Sequence assembly + - Transcriptomics + - Sequence analysis + Galaxy tool ids: + - busco + Galaxy wrapper id: busco + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ + Galaxy wrapper version: 5.7.1 + No. of tool users (5 years) (usegalaxy.eu): 102717 + No. of tool users (5 years) (usegalaxy.org): 34251 + No. of tool users (5 years) (usegalaxy.org.au): 33192 + No. of tool users (5 years) - all main servers: 170160 + No. of tool users (all time) (usegalaxy.eu): 103051 + No. of tool users (all time) (usegalaxy.org): 34251 + No. of tool users (all time) (usegalaxy.org.au): 34369 + No. of tool users (all time) - all main servers: 171671 + Source: https://gitlab.com/ezlab/busco/-/releases + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3877 + Tool usage (5 years) (usegalaxy.org): 3506 + Tool usage (5 years) (usegalaxy.org.au): 2439 + Tool usage (5 years) - all main servers: 9822 + Tool usage (all time) (usegalaxy.eu): 3926 + Tool usage (all time) (usegalaxy.org): 3506 + Tool usage (all time) (usegalaxy.org.au): 2525 + Tool usage (all time) - all main servers: 9957 + ToolShed categories: + - Sequence Analysis + ToolShed id: busco + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Provides measures for quantitative assessment of genome assembly, + gene set, and transcriptome completeness based on evolutionarily informed expectations + of gene content from near-universal single-copy orthologs. + bio.tool id: busco + bio.tool ids: + - busco + bio.tool name: BUSCO +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: bwa + Conda version: 0.7.18 + Date of first commit of the suite: '2017-11-21' + Description: Wrapper for bwa mem, aln, sampe, and samse + EDAM operation: + - Genome indexing + - Sequence alignment + - Read mapping + - Sequence alignment + - Generation + - Sequence alignment + - Generation + - Sequence alignment + - Sequence alignment + EDAM operation (no superclasses): + - Genome indexing + - Sequence alignment + - Read mapping + - Sequence alignment + - Generation + - Sequence alignment + - Generation + - Sequence alignment + - Sequence alignment + EDAM topic: + - Mapping + EDAM topic (no superclasses): + - Mapping + Galaxy tool ids: + - bwa_mem + - bwa + Galaxy wrapper id: bwa + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa + Galaxy wrapper version: 0.7.18 + No. of tool users (5 years) (usegalaxy.eu): 976935 + No. of tool users (5 years) (usegalaxy.org): 474702 + No. of tool users (5 years) (usegalaxy.org.au): 79802 + No. of tool users (5 years) - all main servers: 1531439 + No. of tool users (all time) (usegalaxy.eu): 1017671 + No. of tool users (all time) (usegalaxy.org): 681286 + No. of tool users (all time) (usegalaxy.org.au): 87191 + No. of tool users (all time) - all main servers: 1786148 + Source: http://bio-bwa.sourceforge.net/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 13526 + Tool usage (5 years) (usegalaxy.org): 32627 + Tool usage (5 years) (usegalaxy.org.au): 4219 + Tool usage (5 years) - all main servers: 50372 + Tool usage (all time) (usegalaxy.eu): 14401 + Tool usage (all time) (usegalaxy.org): 47624 + Tool usage (all time) (usegalaxy.org.au): 4954 + Tool usage (all time) - all main servers: 66979 + ToolShed categories: + - Next Gen Mappers + ToolShed id: bwa + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 2 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Fast, accurate, memory-efficient aligner for short and long + sequencing reads + bio.tool id: bwa + bio.tool ids: + - bwa + bio.tool name: BWA +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bwa-mem2 + Conda version: 2.2.1 + Date of first commit of the suite: '2021-10-08' + Description: Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. + EDAM operation: + - Sequence alignment + EDAM operation (no superclasses): + - Sequence alignment + EDAM topic: + - Mapping + EDAM topic (no superclasses): + - Mapping + Galaxy tool ids: + - bwa_mem2 + Galaxy wrapper id: bwa_mem2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 56619 + No. of tool users (5 years) (usegalaxy.org): 36631 + No. of tool users (5 years) (usegalaxy.org.au): 18121 + No. of tool users (5 years) - all main servers: 111371 + No. of tool users (all time) (usegalaxy.eu): 56619 + No. of tool users (all time) (usegalaxy.org): 36631 + No. of tool users (all time) (usegalaxy.org.au): 18121 + No. of tool users (all time) - all main servers: 111371 + Source: https://github.com/bwa-mem2/bwa-mem2 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2324 + Tool usage (5 years) (usegalaxy.org): 2808 + Tool usage (5 years) (usegalaxy.org.au): 713 + Tool usage (5 years) - all main servers: 5845 + Tool usage (all time) (usegalaxy.eu): 2324 + Tool usage (all time) (usegalaxy.org): 2808 + Tool usage (all time) (usegalaxy.org.au): 713 + Tool usage (all time) - all main servers: 5845 + ToolShed categories: + - Next Gen Mappers + ToolShed id: bwa_mem2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. + It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the + use-case, dataset and the running machine. + bio.tool id: bwa-mem2 + bio.tool ids: + - bwa-mem2 + bio.tool name: Bwa-mem2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bwameth + Conda version: 0.2.7 + Date of first commit of the suite: '2016-09-14' + Description: Fast and accurate alignment of BS-seq reads + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bwameth + Galaxy wrapper id: bwameth + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth + Galaxy wrapper version: 0.2.7 + No. of tool users (5 years) (usegalaxy.eu): 7970 + No. of tool users (5 years) (usegalaxy.org): 5524 + No. of tool users (5 years) (usegalaxy.org.au): 1242 + No. of tool users (5 years) - all main servers: 14736 + No. of tool users (all time) (usegalaxy.eu): 11724 + No. of tool users (all time) (usegalaxy.org): 5524 + No. of tool users (all time) (usegalaxy.org.au): 1242 + No. of tool users (all time) - all main servers: 18490 + Source: https://github.com/brentp/bwa-meth + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 643 + Tool usage (5 years) (usegalaxy.org): 611 + Tool usage (5 years) (usegalaxy.org.au): 114 + Tool usage (5 years) - all main servers: 1368 + Tool usage (all time) (usegalaxy.eu): 826 + Tool usage (all time) (usegalaxy.org): 611 + Tool usage (all time) (usegalaxy.org.au): 114 + Tool usage (all time) - all main servers: 1551 + ToolShed categories: + - Sequence Analysis + - Next Gen Mappers + ToolShed id: bwameth + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 2 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-01-11' + Description: Cactus is a reference-free whole-genome multiple alignment program + EDAM operation: + - Multiple sequence alignment + - Genome alignment + EDAM operation (no superclasses): + - Multiple sequence alignment + - Genome alignment + EDAM topic: + - Genomics + - Sequence analysis + - Phylogeny + - Sequence assembly + - Mapping + - Phylogenetics + EDAM topic (no superclasses): + - Genomics + - Sequence assembly + - Mapping + - Phylogenetics + Galaxy tool ids: + - cactus_cactus + - cactus_export + Galaxy wrapper id: cactus + Galaxy wrapper owner: galaxy-australia + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus + Galaxy wrapper version: 2.7.1 + No. of tool users (5 years) (usegalaxy.eu): 299 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1339 + No. of tool users (5 years) - all main servers: 1638 + No. of tool users (all time) (usegalaxy.eu): 299 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1339 + No. of tool users (all time) - all main servers: 1638 + Source: https://github.com/ComparativeGenomicsToolkit/cactus + Status: To update + Tool usage (5 years) (usegalaxy.eu): 61 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 95 + Tool usage (5 years) - all main servers: 156 + Tool usage (all time) (usegalaxy.eu): 61 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 95 + Tool usage (all time) - all main servers: 156 + ToolShed categories: + - Sequence Analysis + ToolShed id: cactus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Cactus is a reference-free whole-genome multiple alignment + program. + bio.tool id: cactus + bio.tool ids: + - cactus + bio.tool name: Cactus +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2019-08-26' + Description: Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. + The calculated values are then used to set a uniform contrast for all the heatmaps + generated downstream. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - calculate_contrast_threshold + Galaxy wrapper id: calculate_contrast_threshold + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Visualization + - Genomic Interval Operations + - SAM + ToolShed id: calculate_contrast_threshold + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-05-04' + Description: Calculate a numeric parameter value using integer and float values. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - calculate_numeric_param + Galaxy wrapper id: calculate_numeric_param + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 1393 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1393 + No. of tool users (all time) (usegalaxy.eu): 1393 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1393 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 10 + Tool usage (all time) (usegalaxy.eu): 10 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 10 + ToolShed categories: + - Text Manipulation + ToolShed id: calculate_numeric_param + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cami-amber + Conda version: 2.0.7 + Date of first commit of the suite: '2024-05-20' + Description: Evaluation package for the comparative assessment of genome reconstructions + and taxonomic assignments + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - biobox_add_taxid + - cami_amber + - cami_amber_add + - cami_amber_convert + Galaxy wrapper id: cami_amber + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ + Galaxy wrapper version: 2.0.7 + No. of tool users (5 years) (usegalaxy.eu): 195 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 195 + No. of tool users (all time) (usegalaxy.eu): 195 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 195 + Source: https://github.com/CAMI-challenge/AMBER + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Metagenomics + ToolShed id: cami_amber + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 2 + Conda id: cat + Conda version: '5.3' + Date of first commit of the suite: '2019-11-27' + Description: Contig Annotation Tool (CAT) + EDAM operation: + - Taxonomic classification + - Sequence assembly + - Coding region prediction + EDAM operation (no superclasses): + - Taxonomic classification + - Sequence assembly + - Coding region prediction + EDAM topic: + - Metagenomics + - Metagenomic sequencing + - Taxonomy + - Sequence assembly + EDAM topic (no superclasses): + - Metagenomics + - Metagenomic sequencing + - Taxonomy + - Sequence assembly + Galaxy tool ids: + - cat_add_names + - cat_bins + - cat_contigs + - cat_prepare + - cat_summarise + Galaxy wrapper id: cat + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat + Galaxy wrapper version: 5.2.3 + No. of tool users (5 years) (usegalaxy.eu): 3835 + No. of tool users (5 years) (usegalaxy.org): 1359 + No. of tool users (5 years) (usegalaxy.org.au): 646 + No. of tool users (5 years) - all main servers: 5840 + No. of tool users (all time) (usegalaxy.eu): 3835 + No. of tool users (all time) (usegalaxy.org): 1359 + No. of tool users (all time) (usegalaxy.org.au): 646 + No. of tool users (all time) - all main servers: 5840 + Source: https://github.com/dutilh/CAT + Status: To update + Tool usage (5 years) (usegalaxy.eu): 597 + Tool usage (5 years) (usegalaxy.org): 467 + Tool usage (5 years) (usegalaxy.org.au): 98 + Tool usage (5 years) - all main servers: 1162 + Tool usage (all time) (usegalaxy.eu): 597 + Tool usage (all time) (usegalaxy.org): 467 + Tool usage (all time) (usegalaxy.org.au): 98 + Tool usage (all time) - all main servers: 1162 + ToolShed categories: + - Metagenomics + ToolShed id: contig_annotation_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 5 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 2 + biii: null + bio.tool description: Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) + are pipelines for the taxonomic classification of long DNA sequences and metagenome + assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, + as generated by contemporary metagenomics studies. The core algorithm of both + programs involves gene calling, mapping of predicted ORFs against the nr protein + database, and voting-based classification of the entire contig / MAG based on + classification of the individual ORFs. + bio.tool id: cat_bins + bio.tool ids: + - cat_bins + bio.tool name: CAT and BAT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cd-hit + Conda version: 4.8.1 + Date of first commit of the suite: '2018-02-26' + Description: Cluster or compare biological sequence datasets + EDAM operation: + - Sequence clustering + EDAM operation (no superclasses): + - Sequence clustering + EDAM topic: + - Sequencing + EDAM topic (no superclasses): + - Sequencing + Galaxy tool ids: + - cd_hit + Galaxy wrapper id: cdhit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit + Galaxy wrapper version: 4.8.1 + No. of tool users (5 years) (usegalaxy.eu): 10414 + No. of tool users (5 years) (usegalaxy.org): 2 + No. of tool users (5 years) (usegalaxy.org.au): 2 + No. of tool users (5 years) - all main servers: 10418 + No. of tool users (all time) (usegalaxy.eu): 10414 + No. of tool users (all time) (usegalaxy.org): 2 + No. of tool users (all time) (usegalaxy.org.au): 2 + No. of tool users (all time) - all main servers: 10418 + Source: http://weizhongli-lab.org/cd-hit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 510 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 512 + Tool usage (all time) (usegalaxy.eu): 510 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 512 + ToolShed categories: + - Sequence Analysis + - Fasta Manipulation + ToolShed id: cd_hit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Cluster a nucleotide dataset into representative sequences. + bio.tool id: cd-hit + bio.tool ids: + - cd-hit + bio.tool name: cd-hit +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-cemitool + Conda version: 1.26.0 + Date of first commit of the suite: '2022-10-10' + Description: Gene co-expression network analysis tool + EDAM operation: + - Enrichment analysis + - Pathway or network analysis + EDAM operation (no superclasses): + - Enrichment analysis + - Pathway or network analysis + EDAM topic: + - Gene expression + - Transcriptomics + - Microarray experiment + EDAM topic (no superclasses): + - Transcriptomics + - Microarray experiment + Galaxy tool ids: + - cemitool + Galaxy wrapper id: cemitool + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool + Galaxy wrapper version: 1.26.0 + No. of tool users (5 years) (usegalaxy.eu): 225 + No. of tool users (5 years) (usegalaxy.org): 271 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 496 + No. of tool users (all time) (usegalaxy.eu): 225 + No. of tool users (all time) (usegalaxy.org): 271 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 496 + Source: https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 61 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 93 + Tool usage (all time) (usegalaxy.eu): 32 + Tool usage (all time) (usegalaxy.org): 61 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 93 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: cemitool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: It unifies the discovery and the analysis of coexpression + gene modules in a fully automatic manner, while providing a user-friendly html + report with high quality graphs. Our tool evaluates if modules contain genes that + are over-represented by specific pathways or that are altered in a specific sample + group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome + information, identifying the potential hubs on each network. + bio.tool id: cemitool + bio.tool ids: + - cemitool + bio.tool name: CEMiTool +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-getopt + Conda version: null + Date of first commit of the suite: '2018-01-30' + Description: Enables advanced visualization options in Galaxy Charts + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - charts + Galaxy wrapper id: charts + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 3383 + No. of tool users (5 years) (usegalaxy.org): 7870 + No. of tool users (5 years) (usegalaxy.org.au): 249 + No. of tool users (5 years) - all main servers: 11502 + No. of tool users (all time) (usegalaxy.eu): 4001 + No. of tool users (all time) (usegalaxy.org): 13727 + No. of tool users (all time) (usegalaxy.org.au): 350 + No. of tool users (all time) - all main servers: 18078 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1576 + Tool usage (5 years) (usegalaxy.org): 3823 + Tool usage (5 years) (usegalaxy.org.au): 108 + Tool usage (5 years) - all main servers: 5507 + Tool usage (all time) (usegalaxy.eu): 1822 + Tool usage (all time) (usegalaxy.org): 6880 + Tool usage (all time) (usegalaxy.org.au): 145 + Tool usage (all time) - all main servers: 8847 + ToolShed categories: + - Visualization + ToolShed id: charts + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 10 + Available on UseGalaxy.fr: 10 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 10 + Conda id: checkm-genome + Conda version: 1.2.3 + Date of first commit of the suite: '2022-07-29' + Description: Assess the quality of microbial genomes recovered from isolates, single + cells, and metagenomes + EDAM operation: + - Sequence assembly validation + - Validation + - Sequence composition calculation + - Sequencing quality control + - Statistical calculation + EDAM operation (no superclasses): + - Sequence assembly validation + - Sequence composition calculation + - Statistical calculation + EDAM topic: + - Genomics + - Phylogenomics + - Phylogenetics + - Taxonomy + - Metagenomics + - Data quality management + EDAM topic (no superclasses): + - Phylogenomics + - Phylogenetics + - Taxonomy + - Metagenomics + - Data quality management + Galaxy tool ids: + - checkm_analyze + - checkm_lineage_set + - checkm_lineage_wf + - checkm_plot + - checkm_qa + - checkm_taxon_set + - checkm_taxonomy_wf + - checkm_tetra + - checkm_tree + - checkm_tree_qa + Galaxy wrapper id: checkm + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm + Galaxy wrapper version: 1.2.3 + No. of tool users (5 years) (usegalaxy.eu): 7500 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7500 + No. of tool users (all time) (usegalaxy.eu): 7500 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7500 + Source: https://github.com/Ecogenomics/CheckM + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 930 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 930 + Tool usage (all time) (usegalaxy.eu): 930 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 930 + ToolShed categories: + - Metagenomics + ToolShed id: checkm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 10 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 10 + Tools available on UseGalaxy.eu: 10 + Tools available on UseGalaxy.fr: 10 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 10 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 10 + UseGalaxy.eu: 10 + UseGalaxy.fr: 10 + UseGalaxy.or: 10 + biii: null + bio.tool description: CheckM provides a set of tools for assessing the quality of + genomes recovered from isolates, single cells, or metagenomes. + bio.tool id: checkm + bio.tool ids: + - checkm + bio.tool name: CheckM +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cherri + Conda version: '0.8' + Date of first commit of the suite: '2022-12-09' + Description: Computational Help Evaluating RNA-RNA interactions + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Molecular interactions, pathways and networks + - Structure analysis + - Machine learning + EDAM topic (no superclasses): + - Molecular interactions, pathways and networks + - Structure analysis + - Machine learning + Galaxy tool ids: + - cherri_eval + - cherri_train + Galaxy wrapper id: cherri + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri + Galaxy wrapper version: '0.7' + No. of tool users (5 years) (usegalaxy.eu): 207 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 207 + No. of tool users (all time) (usegalaxy.eu): 207 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 207 + Source: https://github.com/BackofenLab/Cherri + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Transcriptomics + - RNA + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + biii: null + bio.tool description: CheRRI detects functional RNA-RNA interaction (RRI) sites, + by evaluating if an interaction site most likely occurs in nature. It helps to + filter interaction sites generated either experimentally or by an RRI prediction + algorithm by removing false positive interactions. + bio.tool id: cherri + bio.tool ids: + - cherri + bio.tool name: cherri +- Available on UseGalaxy.eu: 8 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: chewbbaca + Conda version: 3.3.10 + Date of first commit of the suite: '2024-04-13' + Description: BSR-Based Allele Calling Algorithm + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - chewbbaca_allelecall + - chewbbaca_allelecallevaluator + - chewbbaca_createschema + - chewbbaca_downloadschema + - chewbbaca_extractcgmlst + - chewbbaca_joinprofiles + - chewbbaca_nsstats + - chewbbaca_prepexternalschema + Galaxy wrapper id: chewbbaca + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 727 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 727 + No. of tool users (all time) (usegalaxy.eu): 727 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 727 + Source: https://github.com/B-UMMI/chewBBACA/tree/master + Status: To update + Tool usage (5 years) (usegalaxy.eu): 76 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 76 + Tool usage (all time) (usegalaxy.eu): 76 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 76 + ToolShed categories: + - Variant Analysis + ToolShed id: chewbbaca + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 8 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 8 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: chira + Conda version: 1.4.3 + Date of first commit of the suite: '2020-01-19' + Description: Chimeric Read Annotator for RNA-RNA interactome data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - RNA + - Molecular interactions, pathways and networks + - Functional, regulatory and non-coding RNA + EDAM topic (no superclasses): + - Molecular interactions, pathways and networks + - Functional, regulatory and non-coding RNA + Galaxy tool ids: + - chira_collapse + - chira_extract + - chira_map + - chira_merge + - chira_quantify + Galaxy wrapper id: chira + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira + Galaxy wrapper version: 1.4.3 + No. of tool users (5 years) (usegalaxy.eu): 16542 + No. of tool users (5 years) (usegalaxy.org): 1061 + No. of tool users (5 years) (usegalaxy.org.au): 27 + No. of tool users (5 years) - all main servers: 17630 + No. of tool users (all time) (usegalaxy.eu): 16542 + No. of tool users (all time) (usegalaxy.org): 1061 + No. of tool users (all time) (usegalaxy.org.au): 27 + No. of tool users (all time) - all main servers: 17630 + Source: https://github.com/pavanvidem/chira + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 287 + Tool usage (5 years) (usegalaxy.org): 102 + Tool usage (5 years) (usegalaxy.org.au): 5 + Tool usage (5 years) - all main servers: 394 + Tool usage (all time) (usegalaxy.eu): 287 + Tool usage (all time) (usegalaxy.org): 102 + Tool usage (all time) (usegalaxy.org.au): 5 + Tool usage (all time) - all main servers: 394 + ToolShed categories: + - RNA + - Transcriptomics + - Sequence Analysis + ToolShed id: chira + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: ChiRA is a tool suite to analyze RNA-RNA interactome experimental + data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. + bio.tool id: chira + bio.tool ids: + - chira + bio.tool name: ChiRA +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: chopin2 + Conda version: null + Date of first commit of the suite: '2023-01-18' + Description: Domain-Agnostic Supervised Learning with Hyperdimensional Computing + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - chopin2 + Galaxy wrapper id: chopin2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 + Galaxy wrapper version: 1.0.9.post1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 14 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 14 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 14 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 14 + Source: https://github.com/cumbof/chopin2 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 6 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 6 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Machine Learning + ToolShed id: chopin2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: chromeister + Conda version: 1.5.a + Date of first commit of the suite: '2020-09-30' + Description: ultra-fast pairwise genome comparisons + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - chromeister + Galaxy wrapper id: chromeister + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister + Galaxy wrapper version: 1.5.a + No. of tool users (5 years) (usegalaxy.eu): 2696 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1235 + No. of tool users (5 years) - all main servers: 3931 + No. of tool users (all time) (usegalaxy.eu): 2696 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1235 + No. of tool users (all time) - all main servers: 3931 + Source: https://github.com/estebanpw/chromeister + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 398 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 186 + Tool usage (5 years) - all main servers: 584 + Tool usage (all time) (usegalaxy.eu): 398 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 186 + Tool usage (all time) - all main servers: 584 + ToolShed categories: + - Sequence Analysis + ToolShed id: chromeister + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: circexplorer2 + Conda version: 2.3.8 + Date of first commit of the suite: '2022-08-26' + Description: Comprehensive and integrative circular RNA analysis toolset. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - RNA splicing + - Gene transcripts + - Literature and language + EDAM topic (no superclasses): + - RNA splicing + - Gene transcripts + - Literature and language + Galaxy tool ids: + - circexplorer2 + Galaxy wrapper id: circexplorer2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 + Galaxy wrapper version: 2.3.8 + No. of tool users (5 years) (usegalaxy.eu): 524 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 524 + No. of tool users (all time) (usegalaxy.eu): 524 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 524 + Source: https://github.com/YangLab/CIRCexplorer2 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 32 + Tool usage (all time) (usegalaxy.eu): 32 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 32 + ToolShed categories: + - RNA + - Assembly + ToolShed id: circexplorer2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. + bio.tool id: circexplorer2 + bio.tool ids: + - circexplorer2 + bio.tool name: CIRCexplorer2 +- Available on UseGalaxy.eu: 11 + Available on UseGalaxy.fr: 11 + Available on UseGalaxy.org (Main): 11 + Available on UseGalaxy.org.au: 11 + Conda id: circos + Conda version: 0.69.9 + Date of first commit of the suite: '2020-05-25' + Description: Build Circos Plots in Galaxy + EDAM operation: + - Sequence visualisation + EDAM operation (no superclasses): + - Sequence visualisation + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - circos_aln_to_links + - circos_binlinks + - circos_bundlelinks + - circos + - circos_gc_skew + - circos_resample + - circos_wiggle_to_scatter + - circos_wiggle_to_stacked + - circos_tableviewer + - circos_interval_to_text + - circos_interval_to_tile + Galaxy wrapper id: circos + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos + Galaxy wrapper version: 0.69.8 + No. of tool users (5 years) (usegalaxy.eu): 26265 + No. of tool users (5 years) (usegalaxy.org): 31332 + No. of tool users (5 years) (usegalaxy.org.au): 26359 + No. of tool users (5 years) - all main servers: 83956 + No. of tool users (all time) (usegalaxy.eu): 26265 + No. of tool users (all time) (usegalaxy.org): 31332 + No. of tool users (all time) (usegalaxy.org.au): 26359 + No. of tool users (all time) - all main servers: 83956 + Source: http://circos.ca/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2483 + Tool usage (5 years) (usegalaxy.org): 3535 + Tool usage (5 years) (usegalaxy.org.au): 999 + Tool usage (5 years) - all main servers: 7017 + Tool usage (all time) (usegalaxy.eu): 2483 + Tool usage (all time) (usegalaxy.org): 3535 + Tool usage (all time) (usegalaxy.org.au): 999 + Tool usage (all time) - all main servers: 7017 + ToolShed categories: + - Graphics + ToolShed id: circos + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 11 + Tools available on GalaxyTrakr: 11 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 11 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 11 + Tools available on UseGalaxy.cz: 11 + Tools available on UseGalaxy.eu: 11 + Tools available on UseGalaxy.fr: 11 + Tools available on UseGalaxy.no: 11 + Tools available on UseGalaxy.org (Main): 11 + Tools available on UseGalaxy.org.au: 11 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 11 + UseGalaxy.cz: 11 + UseGalaxy.eu: 11 + UseGalaxy.fr: 11 + UseGalaxy.no: 11 + UseGalaxy.or: 11 + biii: null + bio.tool description: Galactic Circos is a Galaxy wrapper providing a GUI for the + Circos tool. Circos allows visualizing data in a circular format. + bio.tool id: galactic_circos + bio.tool ids: + - galactic_circos + bio.tool name: Galactic Circos +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: cite-seq-count + Conda version: 1.4.5 + Date of first commit of the suite: '2023-01-18' + Description: Count CMO/HTO + EDAM operation: + - RNA-Seq quantification + EDAM operation (no superclasses): + - RNA-Seq quantification + EDAM topic: + - Transcriptomics + - Immunoproteins and antigens + EDAM topic (no superclasses): + - Transcriptomics + - Immunoproteins and antigens + Galaxy tool ids: + - cite_seq_count + Galaxy wrapper id: cite_seq_count + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count + Galaxy wrapper version: 1.4.4 + No. of tool users (5 years) (usegalaxy.eu): 21 + No. of tool users (5 years) (usegalaxy.org): 9 + No. of tool users (5 years) (usegalaxy.org.au): 18 + No. of tool users (5 years) - all main servers: 48 + No. of tool users (all time) (usegalaxy.eu): 21 + No. of tool users (all time) (usegalaxy.org): 9 + No. of tool users (all time) (usegalaxy.org.au): 18 + No. of tool users (all time) - all main servers: 48 + Source: https://github.com/Hoohm/CITE-seq-Count + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 5 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 10 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 5 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 10 + ToolShed categories: + - Single Cell + - Transcriptomics + - Proteomics + ToolShed id: cite_seq_count + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Tool for counting antibody TAGS from a CITE-seq and/or cell + hashing experiment. + bio.tool id: CITE-seq-Count + bio.tool ids: + - CITE-seq-Count + bio.tool name: CITE-seq-Count +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: clair3 + Conda version: 1.0.10 + Date of first commit of the suite: '2022-06-15' + Description: Symphonizing pileup and full-alignment for high-performance long-read + variant calling + EDAM operation: + - Variant calling + EDAM operation (no superclasses): + - Variant calling + EDAM topic: + - Molecular genetics + EDAM topic (no superclasses): + - Molecular genetics + Galaxy tool ids: + - clair3 + Galaxy wrapper id: clair3 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 + Galaxy wrapper version: 1.0.8 + No. of tool users (5 years) (usegalaxy.eu): 3388 + No. of tool users (5 years) (usegalaxy.org): 1 + No. of tool users (5 years) (usegalaxy.org.au): 1 + No. of tool users (5 years) - all main servers: 3390 + No. of tool users (all time) (usegalaxy.eu): 3388 + No. of tool users (all time) (usegalaxy.org): 1 + No. of tool users (all time) (usegalaxy.org.au): 1 + No. of tool users (all time) - all main servers: 3390 + Source: https://github.com/HKU-BAL/Clair3 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 187 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 189 + Tool usage (all time) (usegalaxy.eu): 187 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 189 + ToolShed categories: + - Sequence Analysis + - Variant Analysis + ToolShed id: clair3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'Clair3 is a germline small variant caller for long-reads. + Clair3 makes the best of two major method categories: pileup calling handles most + variant candidates with speed, and full-alignment tackles complicated candidates + to maximize precision and recall. Clair3 runs fast and has superior performance, + especially at lower coverage. Clair3 is simple and modular for easy deployment + and integration.' + bio.tool id: clair3 + bio.tool ids: + - clair3 + bio.tool name: Clair3 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: clustalw + Conda version: '2.1' + Date of first commit of the suite: '2022-10-02' + Description: ClustalW multiple sequence alignment program for DNA or proteins + EDAM operation: + - Multiple sequence alignment + EDAM operation (no superclasses): + - Multiple sequence alignment + EDAM topic: + - Phylogeny + - Sequence analysis + EDAM topic (no superclasses): + - Phylogeny + - Sequence analysis + Galaxy tool ids: + - clustalw + Galaxy wrapper id: clustalw + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw + Galaxy wrapper version: '2.1' + No. of tool users (5 years) (usegalaxy.eu): 79867 + No. of tool users (5 years) (usegalaxy.org): 49493 + No. of tool users (5 years) (usegalaxy.org.au): 8797 + No. of tool users (5 years) - all main servers: 138157 + No. of tool users (all time) (usegalaxy.eu): 80817 + No. of tool users (all time) (usegalaxy.org): 87884 + No. of tool users (all time) (usegalaxy.org.au): 9713 + No. of tool users (all time) - all main servers: 178414 + Source: http://www.clustal.org/clustal2/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1675 + Tool usage (5 years) (usegalaxy.org): 3703 + Tool usage (5 years) (usegalaxy.org.au): 670 + Tool usage (5 years) - all main servers: 6048 + Tool usage (all time) (usegalaxy.eu): 1785 + Tool usage (all time) (usegalaxy.org): 7380 + Tool usage (all time) (usegalaxy.org.au): 728 + Tool usage (all time) - all main servers: 9893 + ToolShed categories: + - Phylogenetics + - Sequence Analysis + ToolShed id: clustalw + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Multiple sequence alignment program with a command-line interface + (Clustal W) and a graphical user interface (Clustal X). The display colours allow + conserved features to be highlighted for easy viewing in the alignment. It is + available for several platforms, including Windows, Macintosh PowerMac, Linux + and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, + ClustalX, Clustal2. + bio.tool id: clustal2 + bio.tool ids: + - clustal2 + bio.tool name: Clustal 2 (Clustal W, Clustal X) +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2024-08-08' + Description: Distance matrix-based hierarchical clustering using SciPy + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - clustering_from_distmat + Galaxy wrapper id: clustering_from_distmat + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ + Galaxy wrapper version: 1.1.1 + No. of tool users (5 years) (usegalaxy.eu): 12 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 12 + No. of tool users (all time) (usegalaxy.eu): 12 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 12 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Statistics + ToolShed id: clustering_from_distmat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cnv-phenopacket + Conda version: null + Date of first commit of the suite: '2024-02-27' + Description: cnv-phenopacket Converts TSV metadata file to JSON. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cnv_phenopacket + Galaxy wrapper id: cnv-phenopacket + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 2 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2 + No. of tool users (all time) (usegalaxy.eu): 2 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2 + Source: https://pypi.org/project/cnv-phenopacket/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Variant Analysis + ToolShed id: cnv_phenopacket + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cnv-vcf2json + Conda version: null + Date of first commit of the suite: '2024-02-27' + Description: cnv-vcf2json Converts structural variants VCF file to JSON. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cnv_vcf2json + Galaxy wrapper id: cnv-vcf2json + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 9 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 9 + No. of tool users (all time) (usegalaxy.eu): 9 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 9 + Source: https://pypi.org/project/cnv-phenopacket/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Variant Analysis + ToolShed id: cnv-vcf2json + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 17 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cnvkit + Conda version: 0.9.11 + Date of first commit of the suite: '2023-05-14' + Description: detecting copy number variants and alterations genome-wide from high-throughput + sequencing + EDAM operation: + - Variant calling + EDAM operation (no superclasses): + - Variant calling + EDAM topic: + - DNA structural variation + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cnvkit_access + - cnvkit_antitarget + - cnvkit_autobin + - cnvkit_batch + - cnvkit_breaks + - cnvkit_call + - cnvkit_coverage + - cnvkit_diagram + - cnvkit_fix + - cnvkit_genemetrics + - cnvkit_heatmap + - cnvkit_reference + - cnvkit_scatter + - cnvkit_segment + - cnvkit_segmetrics + - cnvkit_sex + - cnvkit_target + Galaxy wrapper id: cnvkit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit + Galaxy wrapper version: 0.9.11 + No. of tool users (5 years) (usegalaxy.eu): 618 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 618 + No. of tool users (all time) (usegalaxy.eu): 618 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 618 + Source: https://github.com/etal/cnvkit + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 177 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 177 + Tool usage (all time) (usegalaxy.eu): 177 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 177 + ToolShed categories: + - Variant Analysis + ToolShed id: cnvkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 17 + Tools available on UseGalaxy.eu: 17 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 17 + UseGalaxy.eu: 17 + biii: null + bio.tool description: CNVkit is a software toolkit to infer and visualize copy number + from targeted DNA sequencing data. + bio.tool id: cnvkit + bio.tool ids: + - cnvkit + bio.tool name: CNVkit +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: paml + Conda version: 4.10.7 + Date of first commit of the suite: '2017-07-19' + Description: Detects positive selection + EDAM operation: + - Probabilistic sequence generation + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Phylogenetic tree analysis + EDAM operation (no superclasses): + - Probabilistic sequence generation + EDAM topic: + - Phylogenetics + - Sequence analysis + EDAM topic (no superclasses): + - Phylogenetics + Galaxy tool ids: + - codeml + Galaxy wrapper id: codeml + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml + Galaxy wrapper version: '4.9' + No. of tool users (5 years) (usegalaxy.eu): 61197 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 61197 + No. of tool users (all time) (usegalaxy.eu): 61220 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 61220 + Source: http://abacus.gene.ucl.ac.uk/software/paml.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 64 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 64 + Tool usage (all time) (usegalaxy.eu): 65 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 65 + ToolShed categories: + - Phylogenetics + ToolShed id: codeml + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Package of programs for phylogenetic analyses of DNA or protein + sequences using maximum likelihood. + bio.tool id: paml + bio.tool ids: + - paml + bio.tool name: PAML +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: cojac + Conda version: 0.9.2 + Date of first commit of the suite: '2022-08-11' + Description: co-occurrence of mutations on amplicons + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Genetic variation + EDAM topic (no superclasses): + - Genetic variation + Galaxy tool ids: + - cooc_mutbamscan + - cooc_pubmut + - cooc_tabmut + Galaxy wrapper id: cojac + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac + Galaxy wrapper version: 0.9.2 + No. of tool users (5 years) (usegalaxy.eu): 2758 + No. of tool users (5 years) (usegalaxy.org): 20 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2778 + No. of tool users (all time) (usegalaxy.eu): 2758 + No. of tool users (all time) (usegalaxy.org): 20 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2778 + Source: https://github.com/cbg-ethz/cojac + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 22 + Tool usage (5 years) (usegalaxy.org): 10 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 32 + Tool usage (all time) (usegalaxy.eu): 22 + Tool usage (all time) (usegalaxy.org): 10 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 32 + ToolShed categories: + - Metagenomics + - Sequence Analysis + ToolShed id: cojac + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.or: 2 + biii: null + bio.tool description: CoOccurrence adJusted Analysis and Calling - The cojac package + comprises a set of command-line tools to analyse co-occurrence of mutations on + amplicons. It is useful, for example, for early detection of viral variants of + concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed + to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly + by ETH Zurich, EPFL and Eawag. + bio.tool id: cojac + bio.tool ids: + - cojac + bio.tool name: COJAC +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-03-24' + Description: Protein prediction based on AlphaFold2 + EDAM operation: + - Database search + - Protein structure prediction + - Fold recognition + EDAM operation (no superclasses): + - Database search + - Protein structure prediction + - Fold recognition + EDAM topic: + - Protein folds and structural domains + - Protein folding, stability and design + - Structure prediction + - Sequence sites, features and motifs + - Metagenomics + EDAM topic (no superclasses): + - Protein folds and structural domains + - Protein folding, stability and design + - Structure prediction + - Sequence sites, features and motifs + - Metagenomics + Galaxy tool ids: + - colabfold_alphafold + - colabfold_msa + Galaxy wrapper id: colabfold + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold + Galaxy wrapper source: https://github.com/sokrypton/ColabFold + Galaxy wrapper version: 1.5.5 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 6771 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6771 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 6771 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6771 + Source: https://github.com/sokrypton/ColabFold + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 50 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 50 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 50 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 50 + ToolShed categories: + - Proteomics + - Graphics + ToolShed id: colabfold + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 2 + biii: null + bio.tool description: ColabFold databases are MMseqs2 expandable profile databases + to generate diverse multiple sequence alignments to predict protein structures. + bio.tool id: Colabfold + bio.tool ids: + - Colabfold + bio.tool name: ColabFold +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: commet + Conda version: 24.7.14 + Date of first commit of the suite: '2017-10-06' + Description: Colib'read tools are all dedicated to the analysis of NGS datasets + without the need of any reference genome + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - commet + - discosnp_rad + - discosnp_pp + - kissplice + - lordec + - mapsembler2 + - takeabreak + Galaxy wrapper id: colibread + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread + Galaxy wrapper version: 24.7.14 + No. of tool users (5 years) (usegalaxy.eu): 273 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 273 + No. of tool users (all time) (usegalaxy.eu): 273 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 273 + Source: https://colibread.inria.fr/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 40 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 40 + Tool usage (all time) (usegalaxy.eu): 40 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 40 + ToolShed categories: + - Sequence Analysis + - Variant Analysis + ToolShed id: colibread + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: coreutils + Conda version: '8.25' + Date of first commit of the suite: '2016-05-26' + Description: Column Join on Collections + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - collection_column_join + Galaxy wrapper id: collection_column_join + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join + Galaxy wrapper version: 0.0.3 + No. of tool users (5 years) (usegalaxy.eu): 23979 + No. of tool users (5 years) (usegalaxy.org): 21671 + No. of tool users (5 years) (usegalaxy.org.au): 2939 + No. of tool users (5 years) - all main servers: 48589 + No. of tool users (all time) (usegalaxy.eu): 25337 + No. of tool users (all time) (usegalaxy.org): 25163 + No. of tool users (all time) (usegalaxy.org.au): 3036 + No. of tool users (all time) - all main servers: 53536 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3827 + Tool usage (5 years) (usegalaxy.org): 4645 + Tool usage (5 years) (usegalaxy.org.au): 688 + Tool usage (5 years) - all main servers: 9160 + Tool usage (all time) (usegalaxy.eu): 4011 + Tool usage (all time) (usegalaxy.org): 5045 + Tool usage (all time) (usegalaxy.org.au): 701 + Tool usage (all time) - all main servers: 9757 + ToolShed categories: + - Text Manipulation + ToolShed id: collection_column_join + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2018-06-13' + Description: Extract element identifiers of a collection + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - collection_element_identifiers + Galaxy wrapper id: collection_element_identifiers + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers + Galaxy wrapper version: 0.0.2 + No. of tool users (5 years) (usegalaxy.eu): 6905 + No. of tool users (5 years) (usegalaxy.org): 7761 + No. of tool users (5 years) (usegalaxy.org.au): 1157 + No. of tool users (5 years) - all main servers: 15823 + No. of tool users (all time) (usegalaxy.eu): 7102 + No. of tool users (all time) (usegalaxy.org): 7761 + No. of tool users (all time) (usegalaxy.org.au): 1157 + No. of tool users (all time) - all main servers: 16020 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1620 + Tool usage (5 years) (usegalaxy.org): 1897 + Tool usage (5 years) (usegalaxy.org.au): 243 + Tool usage (5 years) - all main servers: 3760 + Tool usage (all time) (usegalaxy.eu): 1630 + Tool usage (all time) (usegalaxy.org): 1897 + Tool usage (all time) (usegalaxy.org.au): 243 + Tool usage (all time) - all main servers: 3770 + ToolShed categories: + - Text Manipulation + ToolShed id: collection_element_identifiers + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-06-24' + Description: Compute an expression on every row + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - Add_a_column1 + Galaxy wrapper id: column_maker + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker + Galaxy wrapper version: '2.1' + No. of tool users (5 years) (usegalaxy.eu): 2940752 + No. of tool users (5 years) (usegalaxy.org): 263254 + No. of tool users (5 years) (usegalaxy.org.au): 96478 + No. of tool users (5 years) - all main servers: 3300484 + No. of tool users (all time) (usegalaxy.eu): 3907183 + No. of tool users (all time) (usegalaxy.org): 737503 + No. of tool users (all time) (usegalaxy.org.au): 97667 + No. of tool users (all time) - all main servers: 4742353 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5422 + Tool usage (5 years) (usegalaxy.org): 6095 + Tool usage (5 years) (usegalaxy.org.au): 884 + Tool usage (5 years) - all main servers: 12401 + Tool usage (all time) (usegalaxy.eu): 6121 + Tool usage (all time) (usegalaxy.org): 13728 + Tool usage (all time) (usegalaxy.org.au): 974 + Tool usage (all time) - all main servers: 20823 + ToolShed categories: + - Text Manipulation + ToolShed id: column_maker + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 1 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2017-04-04' + Description: Sort Column Order by heading + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - column_order_header_sort + Galaxy wrapper id: column_order_header_sort + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 3735 + No. of tool users (5 years) (usegalaxy.org): 1923 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5658 + No. of tool users (all time) (usegalaxy.eu): 3891 + No. of tool users (all time) (usegalaxy.org): 1923 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5814 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort + Status: To update + Tool usage (5 years) (usegalaxy.eu): 268 + Tool usage (5 years) (usegalaxy.org): 381 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 649 + Tool usage (all time) (usegalaxy.eu): 297 + Tool usage (all time) (usegalaxy.org): 381 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 678 + ToolShed categories: + - Text Manipulation + ToolShed id: column_order_header_sort + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2017-04-04' + Description: Remove columns by header + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - column_remove_by_header + Galaxy wrapper id: column_remove_by_header + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 8331 + No. of tool users (5 years) (usegalaxy.org): 5206 + No. of tool users (5 years) (usegalaxy.org.au): 1976 + No. of tool users (5 years) - all main servers: 15513 + No. of tool users (all time) (usegalaxy.eu): 8917 + No. of tool users (all time) (usegalaxy.org): 5206 + No. of tool users (all time) (usegalaxy.org.au): 1976 + No. of tool users (all time) - all main servers: 16099 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header + Status: To update + Tool usage (5 years) (usegalaxy.eu): 613 + Tool usage (5 years) (usegalaxy.org): 716 + Tool usage (5 years) (usegalaxy.org.au): 27 + Tool usage (5 years) - all main servers: 1356 + Tool usage (all time) (usegalaxy.eu): 662 + Tool usage (all time) (usegalaxy.org): 716 + Tool usage (all time) (usegalaxy.org.au): 27 + Tool usage (all time) - all main servers: 1405 + ToolShed categories: + - Text Manipulation + ToolShed id: column_remove_by_header + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: compleasm + Conda version: 0.2.6 + Date of first commit of the suite: '2023-12-04' + Description: 'Compleasm: a faster and more accurate reimplementation of BUSCO' + EDAM operation: + - Sequence assembly validation + - Sequence analysis + - Scaffolding + - Transcriptome assembly + EDAM operation (no superclasses): + - Sequence assembly validation + - Sequence analysis + - Scaffolding + - Transcriptome assembly + EDAM topic: + - Sequence assembly + - Genomics + - Transcriptomics + - Sequence analysis + EDAM topic (no superclasses): + - Sequence assembly + - Transcriptomics + - Sequence analysis + Galaxy tool ids: + - compleasm + Galaxy wrapper id: compleasm + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ + Galaxy wrapper version: 0.2.6 + No. of tool users (5 years) (usegalaxy.eu): 266 + No. of tool users (5 years) (usegalaxy.org): 28 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 294 + No. of tool users (all time) (usegalaxy.eu): 266 + No. of tool users (all time) (usegalaxy.org): 28 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 294 + Source: https://github.com/huangnengCSU/compleasm + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 39 + Tool usage (5 years) (usegalaxy.org): 15 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 54 + Tool usage (all time) (usegalaxy.eu): 39 + Tool usage (all time) (usegalaxy.org): 15 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 54 + ToolShed categories: + - Sequence Analysis + ToolShed id: compleasm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: '"Compleasm: a faster and more accurate reimplementation of + BUSCO"' + bio.tool id: compleasm + bio.tool ids: + - compleasm + bio.tool name: compleasm +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2019-05-09' + Description: Compose a text parameter value using text, integer and float values + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - compose_text_param + Galaxy wrapper id: compose_text_param + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param + Galaxy wrapper version: 0.1.1 + No. of tool users (5 years) (usegalaxy.eu): 45827 + No. of tool users (5 years) (usegalaxy.org): 7721 + No. of tool users (5 years) (usegalaxy.org.au): 1481 + No. of tool users (5 years) - all main servers: 55029 + No. of tool users (all time) (usegalaxy.eu): 45831 + No. of tool users (all time) (usegalaxy.org): 7721 + No. of tool users (all time) (usegalaxy.org.au): 1481 + No. of tool users (all time) - all main servers: 55033 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 689 + Tool usage (5 years) (usegalaxy.org): 303 + Tool usage (5 years) (usegalaxy.org.au): 121 + Tool usage (5 years) - all main servers: 1113 + Tool usage (all time) (usegalaxy.eu): 691 + Tool usage (all time) (usegalaxy.org): 303 + Tool usage (all time) (usegalaxy.org.au): 121 + Tool usage (all time) - all main servers: 1115 + ToolShed categories: + - Text Manipulation + ToolShed id: compose_text_param + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: gzip + Conda version: null + Date of first commit of the suite: '2022-02-04' + Description: Compress files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - compress_file + Galaxy wrapper id: compress_file + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 6343 + No. of tool users (5 years) (usegalaxy.org): 3674 + No. of tool users (5 years) (usegalaxy.org.au): 11832 + No. of tool users (5 years) - all main servers: 21849 + No. of tool users (all time) (usegalaxy.eu): 6343 + No. of tool users (all time) (usegalaxy.org): 3674 + No. of tool users (all time) (usegalaxy.org.au): 11832 + No. of tool users (all time) - all main servers: 21849 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file + Status: To update + Tool usage (5 years) (usegalaxy.eu): 290 + Tool usage (5 years) (usegalaxy.org): 286 + Tool usage (5 years) (usegalaxy.org.au): 59 + Tool usage (5 years) - all main servers: 635 + Tool usage (all time) (usegalaxy.eu): 290 + Tool usage (all time) (usegalaxy.org): 286 + Tool usage (all time) (usegalaxy.org.au): 59 + Tool usage (all time) - all main servers: 635 + ToolShed categories: + - Text Manipulation + ToolShed id: compress_file + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: concoct + Conda version: 1.1.0 + Date of first commit of the suite: '2022-02-18' + Description: CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised + binning of metagenomic contigs byusing nucleotide composition - kmer frequencies + - and coverage data for multiple samples. CONCOCT can accurately(up to species + level) bin metagenomic contigs. + EDAM operation: + - Sequence clustering + - Read binning + EDAM operation (no superclasses): + - Sequence clustering + - Read binning + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - concoct + - concoct_coverage_table + - concoct_cut_up_fasta + - concoct_extract_fasta_bins + - concoct_merge_cut_up_clustering + Galaxy wrapper id: concoct + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 2105 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2105 + No. of tool users (all time) (usegalaxy.eu): 2105 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2105 + Source: https://github.com/BinPro/CONCOCT + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 155 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 155 + Tool usage (all time) (usegalaxy.eu): 155 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 155 + ToolShed categories: + - Metagenomics + ToolShed id: concoct + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + biii: null + bio.tool description: A program for unsupervised binning of metagenomic contigs + by using nucleotide composition, coverage data in multiple samples and linkage + data from paired end reads. + bio.tool id: concoct + bio.tool ids: + - concoct + bio.tool name: CONCOCT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cosg + Conda version: 1.0.1 + Date of first commit of the suite: '2024-05-29' + Description: Marker gene identification for single-cell sequencing data using COSG. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cosg + Galaxy wrapper id: cosg + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/genecell/COSG + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Transcriptomics + - Sequence Analysis + - Single Cell + ToolShed id: cosg + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-number-format + Conda version: '1.76' + Date of first commit of the suite: '2017-10-16' + Description: Generate Detailed Coverage Report from BAM file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - CoverageReport2 + Galaxy wrapper id: coverage_report + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report + Galaxy wrapper version: 0.0.4 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/galaxyproject/tools-iuc + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: coverage_report + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: coverm + Conda version: 0.7.0 + Date of first commit of the suite: '2022-04-26' + Description: CoverM genome and contig wrappers + EDAM operation: + - Local alignment + EDAM operation (no superclasses): + - Local alignment + EDAM topic: + - Bioinformatics + EDAM topic (no superclasses): + - Bioinformatics + Galaxy tool ids: + - coverm_contig + - coverm_genome + Galaxy wrapper id: coverm + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tools/coverm + Galaxy wrapper version: 0.7.0 + No. of tool users (5 years) (usegalaxy.eu): 1081 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1081 + No. of tool users (all time) (usegalaxy.eu): 1081 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1081 + Source: https://github.com/wwood/CoverM + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 151 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 151 + Tool usage (all time) (usegalaxy.eu): 151 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 151 + ToolShed categories: + - Sequence Analysis + ToolShed id: coverm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + biii: null + bio.tool description: Read coverage calculator for metagenomics + bio.tool id: coverm + bio.tool ids: + - coverm + bio.tool name: CoverM +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: crispr_studio + Conda version: '1' + Date of first commit of the suite: '2019-08-13' + Description: CRISPR Studio is a program developed to facilitate and accelerate CRISPR + array visualization. + EDAM operation: + - Visualisation + EDAM operation (no superclasses): + - Visualisation + EDAM topic: + - Sequence analysis + - Genomics + - Data visualisation + EDAM topic (no superclasses): + - Sequence analysis + - Genomics + - Data visualisation + Galaxy tool ids: + - crispr_studio + Galaxy wrapper id: crispr_studio + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ + Galaxy wrapper version: 1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 1052 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1052 + No. of tool users (all time) (usegalaxy.eu): 1053 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1053 + Source: https://github.com/moineaulab/CRISPRStudio + Status: To update + Tool usage (5 years) (usegalaxy.eu): 75 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 75 + Tool usage (all time) (usegalaxy.eu): 76 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 76 + ToolShed categories: + - Sequence Analysis + ToolShed id: crispr_studio + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: CRISPRStudio is a program developed to facilitate and accelerate + CRISPR array visualization. It works by first comparing spacers sequence homology + in a dataset, then assigning a two-color-code to each cluster of spacers and finally + writing an svg file, which can be opened in graphics vector editor. + bio.tool id: crisprstudio + bio.tool ids: + - crisprstudio + bio.tool name: CRISPRStudio +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: r-ggplot2 + Conda version: 2.2.1 + Date of first commit of the suite: '2018-07-27' + Description: Barcode contamination discovery tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - crosscontamination_barcode_filter + Galaxy wrapper id: crosscontamination_barcode_filter + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter + Galaxy wrapper version: '0.3' + No. of tool users (5 years) (usegalaxy.eu): 276 + No. of tool users (5 years) (usegalaxy.org): 131 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 407 + No. of tool users (all time) (usegalaxy.eu): 390 + No. of tool users (all time) (usegalaxy.org): 131 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 521 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 61 + Tool usage (5 years) (usegalaxy.org): 42 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 103 + Tool usage (all time) (usegalaxy.eu): 76 + Tool usage (all time) (usegalaxy.org): 42 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 118 + ToolShed categories: + - Transcriptomics + - Visualization + ToolShed id: crosscontamination_barcode_filter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 0 + Conda id: crossmap + Conda version: 0.7.0 + Date of first commit of the suite: '2017-07-02' + Description: CrossMap converts genome coordinates or annotation files between genome + assemblies + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - crossmap_bam + - crossmap_bed + - crossmap_bw + - crossmap_gff + - crossmap_region + - crossmap_vcf + - crossmap_wig + Galaxy wrapper id: crossmap + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap + Galaxy wrapper version: 0.7.0 + No. of tool users (5 years) (usegalaxy.eu): 2182 + No. of tool users (5 years) (usegalaxy.org): 5251 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7433 + No. of tool users (all time) (usegalaxy.eu): 2182 + No. of tool users (all time) (usegalaxy.org): 5251 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7433 + Source: http://crossmap.sourceforge.net/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 331 + Tool usage (5 years) (usegalaxy.org): 903 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1234 + Tool usage (all time) (usegalaxy.eu): 331 + Tool usage (all time) (usegalaxy.org): 903 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1234 + ToolShed categories: + - Convert Formats + - Genomic Interval Operations + ToolShed id: crossmap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 5 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.fr: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: cutadapt + Conda version: '4.9' + Date of first commit of the suite: '2023-11-03' + Description: Flexible tool to remove adapter sequences (and quality trim) high throughput + sequencing reads (fasta/fastq). + EDAM operation: + - Sequence trimming + - Primer removal + - Read pre-processing + EDAM operation (no superclasses): + - Sequence trimming + - Primer removal + - Read pre-processing + EDAM topic: + - Genomics + - Probes and primers + - Sequencing + EDAM topic (no superclasses): + - Genomics + - Probes and primers + - Sequencing + Galaxy tool ids: + - cutadapt + Galaxy wrapper id: cutadapt + Galaxy wrapper owner: lparsons + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt + Galaxy wrapper version: '4.9' + No. of tool users (5 years) (usegalaxy.eu): 259754 + No. of tool users (5 years) (usegalaxy.org): 334550 + No. of tool users (5 years) (usegalaxy.org.au): 64377 + No. of tool users (5 years) - all main servers: 658681 + No. of tool users (all time) (usegalaxy.eu): 272370 + No. of tool users (all time) (usegalaxy.org): 362356 + No. of tool users (all time) (usegalaxy.org.au): 65986 + No. of tool users (all time) - all main servers: 700712 + Source: https://cutadapt.readthedocs.org/en/stable/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 11716 + Tool usage (5 years) (usegalaxy.org): 18618 + Tool usage (5 years) (usegalaxy.org.au): 3507 + Tool usage (5 years) - all main servers: 33841 + Tool usage (all time) (usegalaxy.eu): 12601 + Tool usage (all time) (usegalaxy.org): 20162 + Tool usage (all time) (usegalaxy.org.au): 3627 + Tool usage (all time) - all main servers: 36390 + ToolShed categories: + - Fasta Manipulation + - Fastq Manipulation + - Sequence Analysis + ToolShed id: cutadapt + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Find and remove adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. + bio.tool id: cutadapt + bio.tool ids: + - cutadapt + bio.tool name: Cutadapt +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: cutesv + Conda version: 2.1.1 + Date of first commit of the suite: '2020-09-23' + Description: Long-read sequencing enables the comprehensive discovery of structural + variations (SVs). However, it is still non-trivial to achieve high sensitivity + and performance simultaneously due to the complex SV characteristics implied by + noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable + long-read-based SV detection approach. cuteSV uses tailored methods to collect + the signatures of various types of SVs and employs a clustering-and-refinement + method to analyze the signatures to implement sensitive SV detection. Benchmarks + on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets + demonstrate that cuteSV has better yields and scalability than state-of-the-art + tools. + EDAM operation: + - Split read mapping + - Genotyping + - Structural variation detection + EDAM operation (no superclasses): + - Split read mapping + - Genotyping + - Structural variation detection + EDAM topic: + - DNA structural variation + - Sequencing + - Computer science + EDAM topic (no superclasses): + - Sequencing + - Computer science + Galaxy tool ids: + - cutesv + Galaxy wrapper id: cutesv + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv + Galaxy wrapper version: 2.1.1 + No. of tool users (5 years) (usegalaxy.eu): 260 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 119 + No. of tool users (5 years) - all main servers: 379 + No. of tool users (all time) (usegalaxy.eu): 260 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 119 + No. of tool users (all time) - all main servers: 379 + Source: https://github.com/tjiangHIT/cuteSV + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 43 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 8 + Tool usage (5 years) - all main servers: 51 + Tool usage (all time) (usegalaxy.eu): 43 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 8 + Tool usage (all time) - all main servers: 51 + ToolShed categories: + - Variant Analysis + ToolShed id: cutesv + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Long Read based Human Genomic Structural Variation Detection + with cuteSV | Long-read sequencing technologies enable to comprehensively discover + structural variations (SVs). However, it is still non-trivial for state-of-the-art + approaches to detect SVs with high sensitivity or high performance or both. Herein, + we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV + uses tailored methods to comprehensively collect various types of SV signatures, + and a clustering-and-refinement method to implement a stepwise SV detection, which + enables to achieve high sensitivity without loss of accuracy. Benchmark results + demonstrate that cuteSV has better yields on real datasets. Further, its speed + and scalability are outstanding and promising to large-scale data analysis + bio.tool id: cuteSV + bio.tool ids: + - cuteSV + bio.tool name: cuteSV +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: matplotlib + Conda version: null + Date of first commit of the suite: '2015-12-18' + Description: Contains a tool that takes a list of called peaks on both strands and + produces a list of matched pairsand a list of unmatched orphans. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cwpair2 + Galaxy wrapper id: cwpair2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 + Galaxy wrapper version: 1.1.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 173 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 173 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 280 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 280 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 41 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 41 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 83 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 83 + ToolShed categories: + - ChIP-seq + ToolShed id: cwpair2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 10 + Available on UseGalaxy.fr: 10 + Available on UseGalaxy.org (Main): 10 + Available on UseGalaxy.org.au: 10 + Conda id: bioconductor-dada2 + Conda version: 1.30.0 + Date of first commit of the suite: '2019-07-05' + Description: DADA2 wrappers + EDAM operation: + - Variant calling + - DNA barcoding + EDAM operation (no superclasses): + - Variant calling + - DNA barcoding + EDAM topic: + - Sequencing + - Genetic variation + - Microbial ecology + - Metagenomics + EDAM topic (no superclasses): + - Sequencing + - Genetic variation + - Microbial ecology + - Metagenomics + Galaxy tool ids: + - dada2_assignTaxonomyAddspecies + - dada2_dada + - dada2_filterAndTrim + - dada2_learnErrors + - dada2_makeSequenceTable + - dada2_mergePairs + - dada2_plotComplexity + - dada2_plotQualityProfile + - dada2_removeBimeraDenovo + - dada2_seqCounts + Galaxy wrapper id: dada2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 92240 + No. of tool users (5 years) (usegalaxy.org): 179176 + No. of tool users (5 years) (usegalaxy.org.au): 12478 + No. of tool users (5 years) - all main servers: 283894 + No. of tool users (all time) (usegalaxy.eu): 92240 + No. of tool users (all time) (usegalaxy.org): 179176 + No. of tool users (all time) (usegalaxy.org.au): 12478 + No. of tool users (all time) - all main servers: 283894 + Source: https://benjjneb.github.io/dada2/index.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2716 + Tool usage (5 years) (usegalaxy.org): 5317 + Tool usage (5 years) (usegalaxy.org.au): 394 + Tool usage (5 years) - all main servers: 8427 + Tool usage (all time) (usegalaxy.eu): 2716 + Tool usage (all time) (usegalaxy.org): 5317 + Tool usage (all time) (usegalaxy.org.au): 394 + Tool usage (all time) - all main servers: 8427 + ToolShed categories: + - Metagenomics + ToolShed id: dada2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 10 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 10 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 10 + Tools available on UseGalaxy.cz: 10 + Tools available on UseGalaxy.eu: 10 + Tools available on UseGalaxy.fr: 10 + Tools available on UseGalaxy.no: 10 + Tools available on UseGalaxy.org (Main): 10 + Tools available on UseGalaxy.org.au: 10 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 10 + UseGalaxy.cz: 10 + UseGalaxy.eu: 10 + UseGalaxy.fr: 1 + UseGalaxy.no: 10 + UseGalaxy.or: 10 + biii: null + bio.tool description: This package infers exact sequence variants (SVs) from amplicon + data, replacing the commonly used and coarser OTU clustering approach. This pipeline + inputs demultiplexed fastq files, and outputs the sequence variants and their + sample-wise abundances after removing substitution and chimera errors. Taxonomic + classification is available via a native implementation of the RDP naive Bayesian + classifier. + bio.tool id: dada2 + bio.tool ids: + - dada2 + bio.tool name: dada2 +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: das_tool + Conda version: 1.1.7 + Date of first commit of the suite: '2022-06-23' + Description: DAS Tool for genome resolved metagenomics + EDAM operation: + - Read binning + EDAM operation (no superclasses): + - Read binning + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - Fasta_to_Contig2Bin + - das_tool + Galaxy wrapper id: das_tool + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool + Galaxy wrapper version: 1.1.7 + No. of tool users (5 years) (usegalaxy.eu): 1323 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1323 + No. of tool users (all time) (usegalaxy.eu): 1323 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1323 + Source: https://github.com/cmks/DAS_Tool + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 47 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 47 + Tool usage (all time) (usegalaxy.eu): 47 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 47 + ToolShed categories: + - Metagenomics + ToolShed id: das_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + biii: null + bio.tool description: DAS Tool is an automated method that integrates the results + of a flexible number of binning algorithms to calculate an optimized, non-redundant + set of bins from a single assembly. + bio.tool id: dastool + bio.tool ids: + - dastool + bio.tool name: dastool +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2016-02-18' + Description: IRIS-TCGA Data source tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - data_source_iris_tcga + Galaxy wrapper id: data_source_iris_tcga + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Data Source + ToolShed id: data_source_iris_tcga + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: datamash + Conda version: 1.1.0 + Date of first commit of the suite: '2015-08-03' + Description: 'GNU Datamash is a command-line program which performs basicnumeric,textual + and statistical operations on input textual data files.It is designed to be portable + and reliable, and aid researchersto easily automate analysis pipelines, without + writing code or even short scripts.License: GPL Version 3 (or later).These tool + wrappers were originally writen by Assaf Gordon.' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - datamash_ops + - datamash_reverse + - datamash_transpose + Galaxy wrapper id: datamash + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash + Galaxy wrapper version: '1.8' + No. of tool users (5 years) (usegalaxy.eu): 748586 + No. of tool users (5 years) (usegalaxy.org): 98089 + No. of tool users (5 years) (usegalaxy.org.au): 16235 + No. of tool users (5 years) - all main servers: 862910 + No. of tool users (all time) (usegalaxy.eu): 760943 + No. of tool users (all time) (usegalaxy.org): 112831 + No. of tool users (all time) (usegalaxy.org.au): 16317 + No. of tool users (all time) - all main servers: 890091 + Source: https://www.gnu.org/software/datamash/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7066 + Tool usage (5 years) (usegalaxy.org): 5306 + Tool usage (5 years) (usegalaxy.org.au): 2161 + Tool usage (5 years) - all main servers: 14533 + Tool usage (all time) (usegalaxy.eu): 7307 + Tool usage (all time) (usegalaxy.org): 6131 + Tool usage (all time) (usegalaxy.org.au): 2171 + Tool usage (all time) - all main servers: 15609 + ToolShed categories: + - Text Manipulation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 3 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 1 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-decontam + Conda version: 1.22.0 + Date of first commit of the suite: '2024-09-13' + Description: Removes decontamination features (ASVs/OTUs) using control samples + EDAM operation: + - Classification + EDAM operation (no superclasses): + - Classification + EDAM topic: + - Metagenomics + - Microbial ecology + - Sequencing + EDAM topic (no superclasses): + - Metagenomics + - Microbial ecology + - Sequencing + Galaxy tool ids: + - decontam + Galaxy wrapper id: decontam + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam + Galaxy wrapper version: '1.22' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/benjjneb/decontam + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: decontam + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: Simple statistical identification of contaminating sequence + features in marker-gene or metagenomics data. Works on any kind of feature derived + from environmental sequencing data. Requires DNA quantitation data or sequenced + negative control samples. + bio.tool id: decontam + bio.tool ids: + - decontam + bio.tool name: decontam +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2023-01-09' + Description: Deep Learning method for novel virus detection in sequencing data + EDAM operation: + - Filtering + EDAM operation (no superclasses): + - Filtering + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - decontaminator + Galaxy wrapper id: decontaminator + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 121 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 121 + No. of tool users (all time) (usegalaxy.eu): 121 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 121 + Source: https://github.com/cbib/decontaminator + Status: To update + Tool usage (5 years) (usegalaxy.eu): 28 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 28 + Tool usage (all time) (usegalaxy.eu): 28 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 28 + ToolShed categories: + - Machine Learning + ToolShed id: decontaminator + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Decontaminator is a deep learning helping tool that filters + out phage or fungi contigs from plant virome RNAseq assemblies. + bio.tool id: decontaminator + bio.tool ids: + - decontaminator + bio.tool name: decontaminator +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: deepmicro + Conda version: '1.4' + Date of first commit of the suite: '2023-03-16' + Description: Representation learning and classification framework + EDAM operation: + - Essential dynamics + - Splitting + - Community profiling + EDAM operation (no superclasses): + - Essential dynamics + - Splitting + EDAM topic: + - Microbial ecology + - Machine learning + - Pathology + - Public health and epidemiology + - Allergy, clinical immunology and immunotherapeutics + EDAM topic (no superclasses): + - Microbial ecology + - Machine learning + - Pathology + - Public health and epidemiology + - Allergy, clinical immunology and immunotherapeutics + Galaxy tool ids: + - deepmicro + Galaxy wrapper id: deepmicro + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro + Galaxy wrapper source: https://github.com/paulzierep/DeepMicro + Galaxy wrapper version: '1.4' + No. of tool users (5 years) (usegalaxy.eu): 558 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 558 + No. of tool users (all time) (usegalaxy.eu): 558 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 558 + Source: https://github.com/paulzierep/DeepMicro + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - Machine Learning + ToolShed id: deepmicro + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Deep representation learning for disease prediction based + on microbiome data.DeepMicro is a deep representation learning framework exploiting + various autoencoders to learn robust low-dimensional representations from high-dimensional + data and training classification models based on the learned representation. + bio.tool id: DeepMicro + bio.tool ids: + - DeepMicro + bio.tool name: DeepMicro +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: deepsig + Conda version: 1.2.5 + Date of first commit of the suite: '2023-04-28' + Description: Predictor of signal peptides in proteins based on deep learning + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - deepsig + Galaxy wrapper id: deepsig + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig + Galaxy wrapper version: 1.2.5 + No. of tool users (5 years) (usegalaxy.eu): 65 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 65 + No. of tool users (all time) (usegalaxy.eu): 65 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 65 + Source: https://github.com/BolognaBiocomp/deepsig + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 37 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 37 + Tool usage (all time) (usegalaxy.eu): 37 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 37 + ToolShed categories: + - Genome annotation + ToolShed id: deepsig + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-09-06' + Description: DeepVariant is a deep learning-based variant caller + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - deepvariant + Galaxy wrapper id: deepvariant + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant + Galaxy wrapper version: 1.5.0 + No. of tool users (5 years) (usegalaxy.eu): 2561 + No. of tool users (5 years) (usegalaxy.org): 2916 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5477 + No. of tool users (all time) (usegalaxy.eu): 2561 + No. of tool users (all time) (usegalaxy.org): 2916 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5477 + Source: https://github.com/google/deepvariant + Status: To update + Tool usage (5 years) (usegalaxy.eu): 325 + Tool usage (5 years) (usegalaxy.org): 460 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 785 + Tool usage (all time) (usegalaxy.eu): 325 + Tool usage (all time) (usegalaxy.org): 460 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 785 + ToolShed categories: + - Variant Analysis + ToolShed id: deepvariant + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bedtools + Conda version: 2.31.1 + Date of first commit of the suite: '2018-11-22' + Description: Annotate DESeq2/DEXSeq output tables + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - deg_annotate + Galaxy wrapper id: deg_annotate + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 22774 + No. of tool users (5 years) (usegalaxy.org): 33972 + No. of tool users (5 years) (usegalaxy.org.au): 4236 + No. of tool users (5 years) - all main servers: 60982 + No. of tool users (all time) (usegalaxy.eu): 23146 + No. of tool users (all time) (usegalaxy.org): 33972 + No. of tool users (all time) (usegalaxy.org.au): 4236 + No. of tool users (all time) - all main servers: 61354 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4084 + Tool usage (5 years) (usegalaxy.org): 5372 + Tool usage (5 years) (usegalaxy.org.au): 846 + Tool usage (5 years) - all main servers: 10302 + Tool usage (all time) (usegalaxy.eu): 4155 + Tool usage (all time) (usegalaxy.org): 5372 + Tool usage (all time) (usegalaxy.org.au): 846 + Tool usage (all time) - all main servers: 10373 + ToolShed categories: + - Transcriptomics + ToolShed id: deg_annotate + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: delly + Conda version: 1.3.1 + Date of first commit of the suite: '2020-10-23' + Description: Delly is an integrated structural variant (SV) prediction method that + can discover, genotype and visualize deletions, tandem duplications, inversions + and translocations at single-nucleotide resolution in short-read massively parallel + sequencing data. It uses paired-ends, split-reads and read-depth to sensitively + and accurately delineate genomic rearrangements throughout the genome. + EDAM operation: + - Indel detection + - Structural variation detection + - Variant calling + - Genotyping + - Genetic variation analysis + EDAM operation (no superclasses): + - Indel detection + - Structural variation detection + - Genotyping + EDAM topic: + - DNA structural variation + - Sequencing + - Pathology + - Genomics + - Genetic variation + - Bioinformatics + - Population genomics + - Rare diseases + EDAM topic (no superclasses): + - Sequencing + - Genetic variation + - Bioinformatics + - Population genomics + - Rare diseases + Galaxy tool ids: + - delly_call + - delly_classify + - delly_cnv + - delly_filter + - delly_lr + - delly_merge + Galaxy wrapper id: delly + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly + Galaxy wrapper version: 0.9.1 + No. of tool users (5 years) (usegalaxy.eu): 1451 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1451 + No. of tool users (all time) (usegalaxy.eu): 1451 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1451 + Source: https://github.com/dellytools/delly + Status: To update + Tool usage (5 years) (usegalaxy.eu): 288 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 288 + Tool usage (all time) (usegalaxy.eu): 288 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 288 + ToolShed categories: + - Variant Analysis + ToolShed id: delly + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 3 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 6 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 6 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 6 + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.fr: 6 + biii: null + bio.tool description: Integrated structural variant prediction method that can discover, + genotype and visualize deletions, tandem duplications, inversions and translocations + at single-nucleotide resolution in short-read massively parallel sequencing data. + It uses paired-ends and split-reads to sensitively and accurately delineate genomic + rearrangements throughout the genome. Structural variants can be visualized using + Delly-maze and Delly-suave. + bio.tool id: delly2 + bio.tool ids: + - delly2 + bio.tool name: Delly2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-deseq2 + Conda version: 1.42.0 + Date of first commit of the suite: '2018-11-15' + Description: Differential gene expression analysis based on the negative binomial + distribution + EDAM operation: + - Differential gene expression analysis + - RNA-Seq analysis + EDAM operation (no superclasses): + - Differential gene expression analysis + - RNA-Seq analysis + EDAM topic: + - RNA-Seq + EDAM topic (no superclasses): + - RNA-Seq + Galaxy tool ids: + - deseq2 + Galaxy wrapper id: deseq2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 + Galaxy wrapper version: 2.11.40.8 + No. of tool users (5 years) (usegalaxy.eu): 97434 + No. of tool users (5 years) (usegalaxy.org): 183905 + No. of tool users (5 years) (usegalaxy.org.au): 18551 + No. of tool users (5 years) - all main servers: 299890 + No. of tool users (all time) (usegalaxy.eu): 109474 + No. of tool users (all time) (usegalaxy.org): 246475 + No. of tool users (all time) (usegalaxy.org.au): 20166 + No. of tool users (all time) - all main servers: 376115 + Source: https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11355 + Tool usage (5 years) (usegalaxy.org): 24951 + Tool usage (5 years) (usegalaxy.org.au): 2647 + Tool usage (5 years) - all main servers: 38953 + Tool usage (all time) (usegalaxy.eu): 12514 + Tool usage (all time) (usegalaxy.org): 31957 + Tool usage (all time) (usegalaxy.org.au): 2905 + Tool usage (all time) - all main servers: 47376 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: deseq2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: R/Bioconductor package for differential gene expression analysis + based on the negative binomial distribution. Estimate variance-mean dependence + in count data from high-throughput sequencing assays and test for differential + expression based on a model using the negative binomial distribution. + bio.tool id: DESeq2 + bio.tool ids: + - DESeq2 + bio.tool name: DESeq2 +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: bioconductor-dexseq + Conda version: 1.48.0 + Date of first commit of the suite: '2018-05-02' + Description: Inference of differential exon usage in RNA-Seq + EDAM operation: + - Enrichment analysis + - Exonic splicing enhancer prediction + EDAM operation (no superclasses): + - Enrichment analysis + - Exonic splicing enhancer prediction + EDAM topic: + - RNA-Seq + EDAM topic (no superclasses): + - RNA-Seq + Galaxy tool ids: + - dexseq + - dexseq_count + - plotdexseq + Galaxy wrapper id: dexseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq + Galaxy wrapper version: 1.48.0 + No. of tool users (5 years) (usegalaxy.eu): 14874 + No. of tool users (5 years) (usegalaxy.org): 18475 + No. of tool users (5 years) (usegalaxy.org.au): 3854 + No. of tool users (5 years) - all main servers: 37203 + No. of tool users (all time) (usegalaxy.eu): 16927 + No. of tool users (all time) (usegalaxy.org): 28854 + No. of tool users (all time) (usegalaxy.org.au): 4271 + No. of tool users (all time) - all main servers: 50052 + Source: https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 533 + Tool usage (5 years) (usegalaxy.org): 1403 + Tool usage (5 years) (usegalaxy.org.au): 141 + Tool usage (5 years) - all main servers: 2077 + Tool usage (all time) (usegalaxy.eu): 837 + Tool usage (all time) (usegalaxy.org): 2568 + Tool usage (all time) (usegalaxy.org.au): 163 + Tool usage (all time) - all main servers: 3568 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: dexseq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: The package is focused on finding differential exon usage + using RNA-seq exon counts between samples with different experimental designs. + It provides functions that allows the user to make the necessary statistical tests + based on a model that uses the negative binomial distribution to estimate the + variance between biological replicates and generalized linear models for testing. + The package also provides functions for the visualization and exploration of the + results. + bio.tool id: dexseq + bio.tool ids: + - dexseq + bio.tool name: DEXSeq +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: diamond + Conda version: 2.1.10 + Date of first commit of the suite: '2021-03-21' + Description: DIAMOND is a new alignment tool for aligning short DNA sequencing reads + to a protein reference database such as NCBI-NR. + EDAM operation: + - Sequence alignment analysis + EDAM operation (no superclasses): + - Sequence alignment analysis + EDAM topic: + - Sequence analysis + - Proteins + EDAM topic (no superclasses): + - Sequence analysis + - Proteins + Galaxy tool ids: + - bg_diamond + - bg_diamond_makedb + - bg_diamond_view + Galaxy wrapper id: diamond + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond + Galaxy wrapper version: 2.0.15 + No. of tool users (5 years) (usegalaxy.eu): 61376 + No. of tool users (5 years) (usegalaxy.org): 23164 + No. of tool users (5 years) (usegalaxy.org.au): 63034 + No. of tool users (5 years) - all main servers: 147574 + No. of tool users (all time) (usegalaxy.eu): 61746 + No. of tool users (all time) (usegalaxy.org): 28729 + No. of tool users (all time) (usegalaxy.org.au): 63034 + No. of tool users (all time) - all main servers: 153509 + Source: https://github.com/bbuchfink/diamond + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1847 + Tool usage (5 years) (usegalaxy.org): 1140 + Tool usage (5 years) (usegalaxy.org.au): 522 + Tool usage (5 years) - all main servers: 3509 + Tool usage (all time) (usegalaxy.eu): 1895 + Tool usage (all time) (usegalaxy.org): 1556 + Tool usage (all time) (usegalaxy.org.au): 522 + Tool usage (all time) - all main servers: 3973 + ToolShed categories: + - Sequence Analysis + ToolShed id: diamond + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 3 + Tools available on Galaxy@Pasteur: 3 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 1 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 1 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: Sequence aligner for protein and translated DNA searches and + functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable + for protein-protein search as well as DNA-protein search on short reads and longer + sequences including contigs and assemblies, providing a speedup of BLAST ranging + up to x20,000. + bio.tool id: diamond + bio.tool ids: + - diamond + bio.tool name: Diamond +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-diffbind + Conda version: 3.12.0 + Date of first commit of the suite: '2018-04-07' + Description: Diffbind provides functions for processing ChIP-Seq data. + EDAM operation: + - Differential binding analysis + EDAM operation (no superclasses): + - Differential binding analysis + EDAM topic: + - ChIP-seq + EDAM topic (no superclasses): + - ChIP-seq + Galaxy tool ids: + - diffbind + Galaxy wrapper id: diffbind + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind + Galaxy wrapper version: 3.12.0 + No. of tool users (5 years) (usegalaxy.eu): 7092 + No. of tool users (5 years) (usegalaxy.org): 14367 + No. of tool users (5 years) (usegalaxy.org.au): 1477 + No. of tool users (5 years) - all main servers: 22936 + No. of tool users (all time) (usegalaxy.eu): 7663 + No. of tool users (all time) (usegalaxy.org): 18624 + No. of tool users (all time) (usegalaxy.org.au): 1640 + No. of tool users (all time) - all main servers: 27927 + Source: http://bioconductor.org/packages/release/bioc/html/DiffBind.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 606 + Tool usage (5 years) (usegalaxy.org): 1360 + Tool usage (5 years) (usegalaxy.org.au): 69 + Tool usage (5 years) - all main servers: 2035 + Tool usage (all time) (usegalaxy.eu): 652 + Tool usage (all time) (usegalaxy.org): 1916 + Tool usage (all time) (usegalaxy.org.au): 84 + Tool usage (all time) - all main servers: 2652 + ToolShed categories: + - ChIP-seq + ToolShed id: diffbind + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Compute differentially bound sites from multiple ChIP-seq + experiments using affinity (quantitative) data. Also enables occupancy (overlap) + analysis and plotting functions. + bio.tool id: diffbind + bio.tool ids: + - diffbind + bio.tool name: DiffBind +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: dimet + Conda version: 0.2.4 + Date of first commit of the suite: '2023-10-09' + Description: DIMet is a bioinformatics pipeline for differential analysis of isotopic + targeted labeling data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + - dimet_@EXECUTABLE@ + Galaxy wrapper id: dimet + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet + Galaxy wrapper version: 0.2.4 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/cbib/DIMet + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: disco + Conda version: '1.2' + Date of first commit of the suite: '2017-10-26' + Description: DISCO is a overlap-layout-consensus (OLC) metagenome assembler + EDAM operation: + - Protein sequence analysis + EDAM operation (no superclasses): + - Protein sequence analysis + EDAM topic: + - Structure determination + EDAM topic (no superclasses): + - Structure determination + Galaxy tool ids: + - disco + Galaxy wrapper id: disco + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 358 + No. of tool users (5 years) (usegalaxy.org): 1361 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1719 + No. of tool users (all time) (usegalaxy.eu): 406 + No. of tool users (all time) (usegalaxy.org): 1361 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1767 + Source: http://disco.omicsbio.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 124 + Tool usage (5 years) (usegalaxy.org): 384 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 508 + Tool usage (all time) (usegalaxy.eu): 139 + Tool usage (all time) (usegalaxy.org): 384 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 523 + ToolShed categories: + - Metagenomics + - Assembly + ToolShed id: disco + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: DISCO is software to perform structure determination of protein + homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures + using geometric constraints derived from RDCs and intermolecular distance restraints + such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated + from intramolecular restraints, DISCO guarantees that all satisfying oligomer + structures will be discovered, yet can run in minutes to hours on only a single + desktop-class computer. + bio.tool id: disco + bio.tool ids: + - disco + bio.tool name: DISCO +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: dnabot + Conda version: null + Date of first commit of the suite: '2022-04-17' + Description: DNA assembly using BASIC on OpenTrons + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - dnabot + Galaxy wrapper id: dnabot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot + Galaxy wrapper version: 3.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: dnabot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: dnaweaver_synbiocad + Conda version: 1.0.2 + Date of first commit of the suite: '2022-12-08' + Description: Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - dnaweaver + Galaxy wrapper id: dnaweaver + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/Edinburgh-Genome-Foundry/DnaWeaver + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: dnaweaver + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: dram + Conda version: 1.5.0 + Date of first commit of the suite: '2022-09-01' + Description: DRAM for distilling microbial metabolism to automate the curation of + microbiome function + EDAM operation: + - Gene functional annotation + EDAM operation (no superclasses): + - Gene functional annotation + EDAM topic: + - Metagenomics + - Biological databases + - Molecular genetics + EDAM topic (no superclasses): + - Metagenomics + - Biological databases + - Molecular genetics + Galaxy tool ids: + - dram_annotate + - dram_distill + - dram_merge_annotations + - dram_neighborhoods + - dram_strainer + Galaxy wrapper id: dram + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram + Galaxy wrapper version: 1.5.0 + No. of tool users (5 years) (usegalaxy.eu): 7358 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7358 + No. of tool users (all time) (usegalaxy.eu): 7358 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7358 + Source: https://github.com/WrightonLabCSU/DRAM + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 88 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 88 + Tool usage (all time) (usegalaxy.eu): 88 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 88 + ToolShed categories: + - Metagenomics + ToolShed id: dram + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + biii: null + bio.tool description: 'Distilled and Refined Annotation of Metabolism: A tool for + the annotation and curation of function for microbial and viral genomes' + bio.tool id: dram + bio.tool ids: + - dram + bio.tool name: DRAM +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: drep + Conda version: 3.5.0 + Date of first commit of the suite: '2020-01-06' + Description: dRep compares and dereplicates genome sets + EDAM operation: + - Genome comparison + EDAM operation (no superclasses): + - Genome comparison + EDAM topic: + - Metagenomics + - Genomics + - Sequence analysis + EDAM topic (no superclasses): + - Metagenomics + - Sequence analysis + Galaxy tool ids: + - drep_compare + - drep_dereplicate + Galaxy wrapper id: drep + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep + Galaxy wrapper version: 3.5.0 + No. of tool users (5 years) (usegalaxy.eu): 916 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 916 + No. of tool users (all time) (usegalaxy.eu): 916 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 916 + Source: https://github.com/MrOlm/drep + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 113 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 113 + Tool usage (all time) (usegalaxy.eu): 113 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 113 + ToolShed categories: + - Metagenomics + ToolShed id: drep + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + biii: null + bio.tool description: Fast and accurate genomic comparisons that enables improved + genome recovery from metagenomes through de-replication. + bio.tool id: drep + bio.tool ids: + - drep + bio.tool name: dRep +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-dropletutils + Conda version: 1.22.0 + Date of first commit of the suite: '2019-09-02' + Description: DropletUtils - Utilities for handling droplet-based single-cell RNA-seq + data + EDAM operation: + - Loading + - Community profiling + EDAM operation (no superclasses): [] + EDAM topic: + - Gene expression + - RNA-seq + - Sequencing + - Transcriptomics + EDAM topic (no superclasses): + - Sequencing + - Transcriptomics + Galaxy tool ids: + - dropletutils + Galaxy wrapper id: dropletutils + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ + Galaxy wrapper version: 1.10.0 + No. of tool users (5 years) (usegalaxy.eu): 4413 + No. of tool users (5 years) (usegalaxy.org): 4403 + No. of tool users (5 years) (usegalaxy.org.au): 1816 + No. of tool users (5 years) - all main servers: 10632 + No. of tool users (all time) (usegalaxy.eu): 4442 + No. of tool users (all time) (usegalaxy.org): 4403 + No. of tool users (all time) (usegalaxy.org.au): 1816 + No. of tool users (all time) - all main servers: 10661 + Source: https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 430 + Tool usage (5 years) (usegalaxy.org): 255 + Tool usage (5 years) (usegalaxy.org.au): 33 + Tool usage (5 years) - all main servers: 718 + Tool usage (all time) (usegalaxy.eu): 431 + Tool usage (all time) (usegalaxy.org): 255 + Tool usage (all time) (usegalaxy.org.au): 33 + Tool usage (all time) - all main servers: 719 + ToolShed categories: + - Single Cell + - Sequence Analysis + ToolShed id: dropletutils + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Provides a number of utility functions for handling single-cell + (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data + loading, identification of cells from empty droplets, removal of barcode-swapped + pseudo-cells, and downsampling of the count matrix. + bio.tool id: dropletutils + bio.tool ids: + - dropletutils + bio.tool name: DropletUtils +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: six + Conda version: null + Date of first commit of the suite: '2016-11-29' + Description: Tools to query and download data from several EMBL-EBI databases + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ebi_search_rest_results + Galaxy wrapper id: ebi_tools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools + Galaxy wrapper version: 0.1.1 + No. of tool users (5 years) (usegalaxy.eu): 276 + No. of tool users (5 years) (usegalaxy.org): 1421 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1697 + No. of tool users (all time) (usegalaxy.eu): 406 + No. of tool users (all time) (usegalaxy.org): 1421 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1827 + Source: http://www.ebi.ac.uk/services/all + Status: To update + Tool usage (5 years) (usegalaxy.eu): 133 + Tool usage (5 years) (usegalaxy.org): 547 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 680 + Tool usage (all time) (usegalaxy.eu): 163 + Tool usage (all time) (usegalaxy.org): 547 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 710 + ToolShed categories: + - Web Services + - Data Source + ToolShed id: ebi_tools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-edger + Conda version: 4.0.16 + Date of first commit of the suite: '2019-02-08' + Description: Perform RNA-Seq differential expression analysis using edgeR pipeline + EDAM operation: + - Differential gene expression analysis + EDAM operation (no superclasses): + - Differential gene expression analysis + EDAM topic: + - Genetics + - RNA-Seq + - ChIP-seq + EDAM topic (no superclasses): + - Genetics + - RNA-Seq + - ChIP-seq + Galaxy tool ids: + - edger + Galaxy wrapper id: edger + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger + Galaxy wrapper version: 3.36.0 + No. of tool users (5 years) (usegalaxy.eu): 19294 + No. of tool users (5 years) (usegalaxy.org): 48876 + No. of tool users (5 years) (usegalaxy.org.au): 8010 + No. of tool users (5 years) - all main servers: 76180 + No. of tool users (all time) (usegalaxy.eu): 20905 + No. of tool users (all time) (usegalaxy.org): 58723 + No. of tool users (all time) (usegalaxy.org.au): 8705 + No. of tool users (all time) - all main servers: 88333 + Source: http://bioconductor.org/packages/release/bioc/html/edgeR.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2423 + Tool usage (5 years) (usegalaxy.org): 6341 + Tool usage (5 years) (usegalaxy.org.au): 846 + Tool usage (5 years) - all main servers: 9610 + Tool usage (all time) (usegalaxy.eu): 2618 + Tool usage (all time) (usegalaxy.org): 7527 + Tool usage (all time) (usegalaxy.org.au): 892 + Tool usage (all time) - all main servers: 11037 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: edger + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Differential expression analysis of RNA-seq expression profiles + with biological replication. Implements a range of statistical methodology based + on the negative binomial distributions, including empirical Bayes estimation, + exact tests, generalized linear models and quasi-likelihood tests. As well as + RNA-seq, it be applied to differential signal analysis of other types of genomic + data that produce counts, including ChIP-seq, SAGE and CAGE. + bio.tool id: edger + bio.tool ids: + - edger + bio.tool name: edgeR +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-egsea + Conda version: 1.28.0 + Date of first commit of the suite: '2018-01-01' + Description: This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) + method for gene set testing + EDAM operation: + - Gene set testing + EDAM operation (no superclasses): + - Gene set testing + EDAM topic: + - Systems biology + EDAM topic (no superclasses): + - Systems biology + Galaxy tool ids: + - egsea + Galaxy wrapper id: egsea + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea + Galaxy wrapper version: 1.20.0 + No. of tool users (5 years) (usegalaxy.eu): 2809 + No. of tool users (5 years) (usegalaxy.org): 5179 + No. of tool users (5 years) (usegalaxy.org.au): 1931 + No. of tool users (5 years) - all main servers: 9919 + No. of tool users (all time) (usegalaxy.eu): 3060 + No. of tool users (all time) (usegalaxy.org): 5179 + No. of tool users (all time) (usegalaxy.org.au): 1931 + No. of tool users (all time) - all main servers: 10170 + Source: https://bioconductor.org/packages/release/bioc/html/EGSEA.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 371 + Tool usage (5 years) (usegalaxy.org): 759 + Tool usage (5 years) (usegalaxy.org.au): 226 + Tool usage (5 years) - all main servers: 1356 + Tool usage (all time) (usegalaxy.eu): 402 + Tool usage (all time) (usegalaxy.org): 759 + Tool usage (all time) (usegalaxy.org.au): 226 + Tool usage (all time) - all main servers: 1387 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: egsea + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This package implements the Ensemble of Gene Set Enrichment + Analyses method for gene set testing. + bio.tool id: egsea + bio.tool ids: + - egsea + bio.tool name: EGSEA +- Available on UseGalaxy.eu: 107 + Available on UseGalaxy.fr: 107 + Available on UseGalaxy.org (Main): 107 + Available on UseGalaxy.org.au: 107 + Conda id: emboss + Conda version: 6.6.0 + Date of first commit of the suite: '2017-01-11' + Description: Galaxy wrappers for EMBOSS version 5.0.0 tools + EDAM operation: + - Sequence analysis + - Local alignment + - Sequence alignment analysis + - Global alignment + - Sequence alignment + EDAM operation (no superclasses): + - Sequence analysis + - Local alignment + - Sequence alignment analysis + - Global alignment + - Sequence alignment + EDAM topic: + - Molecular biology + - Sequence analysis + - Biology + EDAM topic (no superclasses): + - Molecular biology + - Sequence analysis + Galaxy tool ids: + - 'EMBOSS: antigenic1' + - 'EMBOSS: backtranseq2' + - 'EMBOSS: banana3' + - 'EMBOSS: biosed4' + - 'EMBOSS: btwisted5' + - 'EMBOSS: cai6' + - 'EMBOSS: cai_custom6' + - 'EMBOSS: chaos7' + - 'EMBOSS: charge8' + - 'EMBOSS: checktrans9' + - 'EMBOSS: chips10' + - 'EMBOSS: cirdna11' + - 'EMBOSS: codcmp12' + - 'EMBOSS: coderet13' + - 'EMBOSS: compseq14' + - 'EMBOSS: cpgplot15' + - 'EMBOSS: cpgreport16' + - 'EMBOSS: cusp17' + - 'EMBOSS: cutseq18' + - 'EMBOSS: dan19' + - 'EMBOSS: degapseq20' + - 'EMBOSS: descseq21' + - 'EMBOSS: diffseq22' + - 'EMBOSS: digest23' + - 'EMBOSS: dotmatcher24' + - 'EMBOSS: dotpath25' + - 'EMBOSS: dottup26' + - 'EMBOSS: dreg27' + - 'EMBOSS: einverted28' + - 'EMBOSS: epestfind29' + - 'EMBOSS: equicktandem31' + - 'EMBOSS: est2genome32' + - 'EMBOSS: etandem33' + - 'EMBOSS: extractfeat34' + - 'EMBOSS: extractseq35' + - 'EMBOSS: freak36' + - 'EMBOSS: fuzznuc37' + - 'EMBOSS: fuzzpro38' + - 'EMBOSS: fuzztran39' + - 'EMBOSS: garnier40' + - 'EMBOSS: geecee41' + - 'EMBOSS: getorf42' + - 'EMBOSS: helixturnhelix43' + - 'EMBOSS: hmoment44' + - 'EMBOSS: iep45' + - 'EMBOSS: infoseq46' + - 'EMBOSS: isochore47' + - 'EMBOSS: lindna48' + - 'EMBOSS: marscan49' + - 'EMBOSS: maskfeat50' + - 'EMBOSS: maskseq51' + - 'EMBOSS: matcher52' + - 'EMBOSS: megamerger53' + - 'EMBOSS: merger54' + - 'EMBOSS: msbar55' + - 'EMBOSS: needle56' + - 'EMBOSS: newcpgreport57' + - 'EMBOSS: newcpgseek58' + - 'EMBOSS: newseq59' + - 'EMBOSS: noreturn60' + - 'EMBOSS: notseq61' + - 'EMBOSS: nthseq62' + - 'EMBOSS: octanol63' + - 'EMBOSS: oddcomp64' + - 'EMBOSS: palindrome65' + - 'EMBOSS: pasteseq66' + - 'EMBOSS: patmatdb67' + - 'EMBOSS: pepcoil68' + - 'EMBOSS: pepinfo69' + - 'EMBOSS: pepnet70' + - 'EMBOSS: pepstats71' + - 'EMBOSS: pepwheel72' + - 'EMBOSS: pepwindow73' + - 'EMBOSS: pepwindowall74' + - 'EMBOSS: plotcon75' + - 'EMBOSS: plotorf76' + - 'EMBOSS: polydot77' + - 'EMBOSS: preg78' + - 'EMBOSS: prettyplot79' + - 'EMBOSS: prettyseq80' + - 'EMBOSS: primersearch81' + - 'EMBOSS: revseq82' + - 'EMBOSS: seqmatchall83' + - 'EMBOSS: seqret84' + - 'EMBOSS: showfeat85' + - 'EMBOSS: shuffleseq87' + - 'EMBOSS: sigcleave88' + - 'EMBOSS: sirna89' + - 'EMBOSS: sixpack90' + - 'EMBOSS: skipseq91' + - 'EMBOSS: splitter92' + - 'EMBOSS: supermatcher95' + - 'EMBOSS: syco96' + - 'EMBOSS: tcode97' + - 'EMBOSS: textsearch98' + - 'EMBOSS: tmap99' + - 'EMBOSS: tranalign100' + - 'EMBOSS: transeq101' + - 'EMBOSS: trimest102' + - 'EMBOSS: trimseq103' + - 'EMBOSS: twofeat104' + - 'EMBOSS: union105' + - 'EMBOSS: vectorstrip106' + - 'EMBOSS: water107' + - 'EMBOSS: wobble108' + - 'EMBOSS: wordcount109' + - 'EMBOSS: wordmatch110' + Galaxy wrapper id: emboss_5 + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 + Galaxy wrapper version: 5.0.0 + No. of tool users (5 years) (usegalaxy.eu): 143762 + No. of tool users (5 years) (usegalaxy.org): 151989 + No. of tool users (5 years) (usegalaxy.org.au): 24955 + No. of tool users (5 years) - all main servers: 320706 + No. of tool users (all time) (usegalaxy.eu): 148864 + No. of tool users (all time) (usegalaxy.org): 296028 + No. of tool users (all time) (usegalaxy.org.au): 27001 + No. of tool users (all time) - all main servers: 471893 + Source: http://emboss.open-bio.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4481 + Tool usage (5 years) (usegalaxy.org): 13224 + Tool usage (5 years) (usegalaxy.org.au): 2397 + Tool usage (5 years) - all main servers: 20102 + Tool usage (all time) (usegalaxy.eu): 5039 + Tool usage (all time) (usegalaxy.org): 31140 + Tool usage (all time) (usegalaxy.org.au): 2705 + Tool usage (all time) - all main servers: 38884 + ToolShed categories: + - Sequence Analysis + - Fasta Manipulation + ToolShed id: emboss_5 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 107 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 107 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 107 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 107 + Tools available on UseGalaxy.cz: 107 + Tools available on UseGalaxy.eu: 107 + Tools available on UseGalaxy.fr: 107 + Tools available on UseGalaxy.no: 107 + Tools available on UseGalaxy.org (Main): 107 + Tools available on UseGalaxy.org.au: 107 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 107 + UseGalaxy.cz: 107 + UseGalaxy.eu: 107 + UseGalaxy.fr: 107 + UseGalaxy.no: 107 + UseGalaxy.or: 107 + biii: null + bio.tool description: Diverse suite of tools for sequence analysis; many programs + analagous to GCG; context-sensitive help for each tool. + bio.tool id: emboss + bio.tool ids: + - emboss + bio.tool name: EMBOSS +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: ena-upload-cli + Conda version: 0.7.4 + Date of first commit of the suite: '2020-11-20' + Description: 'Submits experimental data and respective metadata to the European + Nucleotide Archive (ENA). ' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ena_upload + Galaxy wrapper id: ena_upload + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload + Galaxy wrapper version: 0.7.3 + No. of tool users (5 years) (usegalaxy.eu): 366 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1302 + No. of tool users (5 years) - all main servers: 1668 + No. of tool users (all time) (usegalaxy.eu): 366 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1302 + No. of tool users (all time) - all main servers: 1668 + Source: https://github.com/usegalaxy-eu/ena-upload-cli + Status: To update + Tool usage (5 years) (usegalaxy.eu): 41 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 14 + Tool usage (5 years) - all main servers: 55 + Tool usage (all time) (usegalaxy.eu): 41 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 14 + Tool usage (all time) - all main servers: 55 + ToolShed categories: + - Data Export + ToolShed id: ena_upload + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: enasearch + Conda version: 0.2.2 + Date of first commit of the suite: '2017-08-05' + Description: A Python library for interacting with ENA's API + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - enasearch_retrieve_analysis_report + - enasearch_retrieve_data + - enasearch_retrieve_run_report + - enasearch_retrieve_taxons + - enasearch_search_data + Galaxy wrapper id: enasearch + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 1989 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1989 + No. of tool users (all time) (usegalaxy.eu): 2302 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2302 + Source: https://github.com/bebatut/enasearch + Status: To update + Tool usage (5 years) (usegalaxy.eu): 367 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 367 + Tool usage (all time) (usegalaxy.eu): 453 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 453 + ToolShed categories: + - Data Source + ToolShed id: enasearch + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 4 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 4 + UseGalaxy.no: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ensembl-vep + Conda version: '113.0' + Date of first commit of the suite: '2022-05-11' + Description: 'Ensembl VEP: Annotate VCFs with variant effect predictions' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ensembl_vep + Galaxy wrapper id: ensembl_vep + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep + Galaxy wrapper version: '112.0' + No. of tool users (5 years) (usegalaxy.eu): 3051 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3051 + No. of tool users (all time) (usegalaxy.eu): 3051 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3051 + Source: https://github.com/Ensembl/ensembl-vep + Status: To update + Tool usage (5 years) (usegalaxy.eu): 171 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 171 + Tool usage (all time) (usegalaxy.eu): 171 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 171 + ToolShed categories: + - Variant Analysis + ToolShed id: ensembl_vep + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: episcanpy + Conda version: 0.4.0 + Date of first commit of the suite: '2023-03-22' + Description: "EpiScanpy \u2013 Epigenomics single cell analysis in python" + EDAM operation: + - Enrichment analysis + - Imputation + EDAM operation (no superclasses): + - Enrichment analysis + - Imputation + EDAM topic: + - Epigenomics + - Cell biology + - DNA + EDAM topic (no superclasses): + - Epigenomics + - Cell biology + - DNA + Galaxy tool ids: + - episcanpy_build_matrix + - episcanpy_cluster_embed + - episcanpy_preprocess + Galaxy wrapper id: episcanpy + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ + Galaxy wrapper version: 0.3.2 + No. of tool users (5 years) (usegalaxy.eu): 880 + No. of tool users (5 years) (usegalaxy.org): 221 + No. of tool users (5 years) (usegalaxy.org.au): 49 + No. of tool users (5 years) - all main servers: 1150 + No. of tool users (all time) (usegalaxy.eu): 880 + No. of tool users (all time) (usegalaxy.org): 221 + No. of tool users (all time) (usegalaxy.org.au): 49 + No. of tool users (all time) - all main servers: 1150 + Source: https://github.com/colomemaria/epiScanpy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 80 + Tool usage (5 years) (usegalaxy.org): 37 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 120 + Tool usage (all time) (usegalaxy.eu): 80 + Tool usage (all time) (usegalaxy.org): 37 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 120 + ToolShed categories: + - Single Cell + - Epigenetics + ToolShed id: episcanpy + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: Epigenomics Single Cell Analysis in Python. + bio.tool id: episcanpy + bio.tool ids: + - episcanpy + bio.tool name: epiScanpy +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: evidencemodeler + Conda version: 2.1.0 + Date of first commit of the suite: '2024-07-19' + Description: EVidenceModeler (EVM) combines ab intio genetic predictions with protein + and transcript alignments in weighted consensus genetic structures. + EDAM operation: + - Gene prediction + EDAM operation (no superclasses): + - Gene prediction + EDAM topic: + - Gene expression + - Gene structure + EDAM topic (no superclasses): + - Gene expression + - Gene structure + Galaxy tool ids: + - evidencemodeler + Galaxy wrapper id: evidencemodeler + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler + Galaxy wrapper version: 2.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Genome annotation + ToolShed id: evidencemodeler + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: The EVidenceModeler (aka EVM) software combines ab intio gene + predictions and protein and transcript alignments into weighted consensus gene + structures. EVM provides a flexible and intuitive framework for combining diverse + evidence types into a single automated gene structure annotation system. + bio.tool id: EvidenceModeler + bio.tool ids: + - EvidenceModeler + bio.tool name: EvidenceModeler +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: r-exomedepth + Conda version: 1.1.16 + Date of first commit of the suite: '2019-11-08' + Description: 'ExomeDepth: Calls copy number variants (CNVs) from targeted sequence + data' + EDAM operation: + - Sequence analysis + - Variant calling + - Genotyping + - Copy number estimation + EDAM operation (no superclasses): + - Sequence analysis + - Variant calling + - Genotyping + - Copy number estimation + EDAM topic: + - Exome sequencing + - Gene transcripts + - Mapping + - Sequencing + - Genetic variation + - Rare diseases + EDAM topic (no superclasses): + - Exome sequencing + - Gene transcripts + - Mapping + - Genetic variation + - Rare diseases + Galaxy tool ids: + - exomedepth + Galaxy wrapper id: exomedepth + Galaxy wrapper owner: crs4 + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 517 + No. of tool users (5 years) (usegalaxy.org): 2995 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3512 + No. of tool users (all time) (usegalaxy.eu): 517 + No. of tool users (all time) (usegalaxy.org): 2995 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3512 + Source: https://cran.r-project.org/package=ExomeDepth + Status: To update + Tool usage (5 years) (usegalaxy.eu): 61 + Tool usage (5 years) (usegalaxy.org): 184 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 245 + Tool usage (all time) (usegalaxy.eu): 61 + Tool usage (all time) (usegalaxy.org): 184 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 245 + ToolShed categories: + - Sequence Analysis + - Variant Analysis + ToolShed id: exomedepth + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Copy number variant (CNV) calling algorithm designed to control + technical variability between samples. It calls CNVs from targeted sequence data, + typically exome sequencing experiments designed to identify the genetic basis + of Mendelian disorders. + bio.tool id: exomedepth + bio.tool ids: + - exomedepth + bio.tool name: ExomeDepth +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: exonerate + Conda version: 2.4.0 + Date of first commit of the suite: '2018-08-02' + Description: Exonerate is a generic tool for pairwise sequence comparison. + EDAM operation: + - Pairwise sequence alignment + - Protein threading + - Genome alignment + EDAM operation (no superclasses): + - Pairwise sequence alignment + - Protein threading + - Genome alignment + EDAM topic: + - Sequence analysis + - Sequence sites, features and motifs + - Molecular interactions, pathways and networks + EDAM topic (no superclasses): + - Sequence analysis + - Sequence sites, features and motifs + - Molecular interactions, pathways and networks + Galaxy tool ids: + - exonerate + Galaxy wrapper id: exonerate + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate + Galaxy wrapper version: 2.4.0 + No. of tool users (5 years) (usegalaxy.eu): 1030 + No. of tool users (5 years) (usegalaxy.org): 1058 + No. of tool users (5 years) (usegalaxy.org.au): 922 + No. of tool users (5 years) - all main servers: 3010 + No. of tool users (all time) (usegalaxy.eu): 1072 + No. of tool users (all time) (usegalaxy.org): 1058 + No. of tool users (all time) (usegalaxy.org.au): 922 + No. of tool users (all time) - all main servers: 3052 + Source: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 185 + Tool usage (5 years) (usegalaxy.org): 189 + Tool usage (5 years) (usegalaxy.org.au): 35 + Tool usage (5 years) - all main servers: 409 + Tool usage (all time) (usegalaxy.eu): 188 + Tool usage (all time) (usegalaxy.org): 189 + Tool usage (all time) (usegalaxy.org.au): 35 + Tool usage (all time) - all main servers: 412 + ToolShed categories: + - Sequence Analysis + ToolShed id: exonerate + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool for pairwise sequence alignment. It enables alignment + for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. + bio.tool id: exonerate + bio.tool ids: + - exonerate + bio.tool name: Exonerate +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: export2graphlan + Conda version: '0.22' + Date of first commit of the suite: '2017-03-03' + Description: export2graphlan is a conversion software tool for producing both annotation + and tree file for GraPhlAn + EDAM operation: + - Conversion + EDAM operation (no superclasses): + - Conversion + EDAM topic: + - Taxonomy + - Metabolomics + - Biomarkers + EDAM topic (no superclasses): + - Taxonomy + - Metabolomics + - Biomarkers + Galaxy tool ids: + - export2graphlan + Galaxy wrapper id: export2graphlan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ + Galaxy wrapper version: '0.20' + No. of tool users (5 years) (usegalaxy.eu): 5396 + No. of tool users (5 years) (usegalaxy.org): 628 + No. of tool users (5 years) (usegalaxy.org.au): 519 + No. of tool users (5 years) - all main servers: 6543 + No. of tool users (all time) (usegalaxy.eu): 5938 + No. of tool users (all time) (usegalaxy.org): 628 + No. of tool users (all time) (usegalaxy.org.au): 519 + No. of tool users (all time) - all main servers: 7085 + Source: https://bitbucket.org/CibioCM/export2graphlan/overview + Status: To update + Tool usage (5 years) (usegalaxy.eu): 580 + Tool usage (5 years) (usegalaxy.org): 168 + Tool usage (5 years) (usegalaxy.org.au): 107 + Tool usage (5 years) - all main servers: 855 + Tool usage (all time) (usegalaxy.eu): 607 + Tool usage (all time) (usegalaxy.org): 168 + Tool usage (all time) (usegalaxy.org.au): 107 + Tool usage (all time) - all main servers: 882 + ToolShed categories: + - Metagenomics + ToolShed id: export2graphlan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: export2graphlan is a conversion software tool for producing + both annotation and tree file for GraPhlAn. In particular, the annotation file + tries to highlight specific sub-trees deriving automatically from input file what + nodes are important. + bio.tool id: export2graphlan + bio.tool ids: + - export2graphlan + bio.tool name: export2graphlan +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bx-python + Conda version: 0.13.0 + Date of first commit of the suite: '2016-01-15' + Description: Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED + genomes and UNassembled genomes. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - Extract genomic DNA 1 + Galaxy wrapper id: extract_genomic_dna + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna + Galaxy wrapper version: 3.0.3+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 9409 + No. of tool users (5 years) (usegalaxy.org): 20180 + No. of tool users (5 years) (usegalaxy.org.au): 168 + No. of tool users (5 years) - all main servers: 29757 + No. of tool users (all time) (usegalaxy.eu): 12735 + No. of tool users (all time) (usegalaxy.org): 259099 + No. of tool users (all time) (usegalaxy.org.au): 611 + No. of tool users (all time) - all main servers: 272445 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 813 + Tool usage (5 years) (usegalaxy.org): 2072 + Tool usage (5 years) (usegalaxy.org.au): 20 + Tool usage (5 years) - all main servers: 2905 + Tool usage (all time) (usegalaxy.eu): 923 + Tool usage (all time) (usegalaxy.org): 11791 + Tool usage (all time) (usegalaxy.org.au): 63 + Tool usage (all time) - all main servers: 12777 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: extract_genomic_dna + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 1 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: falco + Conda version: 1.2.4 + Date of first commit of the suite: '2024-04-17' + Description: A high throughput sequence QC analysis tool + EDAM operation: + - Sequencing quality control + - Visualisation + - Read mapping + EDAM operation (no superclasses): + - Sequencing quality control + - Visualisation + - Read mapping + EDAM topic: + - Workflows + - Mapping + - Imaging + EDAM topic (no superclasses): + - Workflows + - Mapping + - Imaging + Galaxy tool ids: + - falco + Galaxy wrapper id: falco + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco + Galaxy wrapper version: 1.2.4 + No. of tool users (5 years) (usegalaxy.eu): 4298 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4298 + No. of tool users (all time) (usegalaxy.eu): 4298 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4298 + Source: https://github.com/smithlabcode/falco/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 34 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 34 + Tool usage (all time) (usegalaxy.eu): 34 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 34 + ToolShed categories: + - Sequence Analysis + ToolShed id: falco + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: A high-speed FastQC emulation for quality control of sequencing + data. + bio.tool id: falco + bio.tool ids: + - falco + bio.tool name: Falco +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: fargene + Conda version: '0.1' + Date of first commit of the suite: '2019-08-30' + Description: fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) + EDAM operation: + - Antimicrobial resistance prediction + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + EDAM topic: + - Metagenomics + - Microbiology + - Public health and epidemiology + EDAM topic (no superclasses): + - Metagenomics + - Microbiology + - Public health and epidemiology + Galaxy tool ids: + - fargene + Galaxy wrapper id: fargene + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 601 + No. of tool users (5 years) (usegalaxy.org): 1165 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1766 + No. of tool users (all time) (usegalaxy.eu): 601 + No. of tool users (all time) (usegalaxy.org): 1165 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1766 + Source: https://github.com/fannyhb/fargene + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 128 + Tool usage (5 years) (usegalaxy.org): 232 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 360 + Tool usage (all time) (usegalaxy.eu): 128 + Tool usage (all time) (usegalaxy.org): 232 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 360 + ToolShed categories: + - Sequence Analysis + ToolShed id: fargene + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr + ) is a tool that takes either fragmented metagenomic data or longer sequences + as input and predicts and delivers full-length antiobiotic resistance genes as + output. + bio.tool id: fargene + bio.tool ids: + - fargene + bio.tool name: fARGene +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: openjdk + Conda version: null + Date of first commit of the suite: '2016-03-06' + Description: Contains a tool that produces a graphical representation of FASTA data + with each nucleotide represented by a selected color. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fasta_nucleotide_color_plot + Galaxy wrapper id: fasta_nucleotide_color_plot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 164 + No. of tool users (5 years) (usegalaxy.org): 758 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 922 + No. of tool users (all time) (usegalaxy.eu): 179 + No. of tool users (all time) (usegalaxy.org): 905 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1084 + Source: https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot + Status: To update + Tool usage (5 years) (usegalaxy.eu): 42 + Tool usage (5 years) (usegalaxy.org): 128 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 170 + Tool usage (all time) (usegalaxy.eu): 47 + Tool usage (all time) (usegalaxy.org): 170 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 217 + ToolShed categories: + - Visualization + ToolShed id: fasta_nucleotide_color_plot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2018-11-21' + Description: Display summary statistics for a fasta file. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fasta-stats + Galaxy wrapper id: fasta_stats + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ + Galaxy wrapper version: '2.0' + No. of tool users (5 years) (usegalaxy.eu): 43726 + No. of tool users (5 years) (usegalaxy.org): 19941 + No. of tool users (5 years) (usegalaxy.org.au): 16788 + No. of tool users (5 years) - all main servers: 80455 + No. of tool users (all time) (usegalaxy.eu): 44512 + No. of tool users (all time) (usegalaxy.org): 19941 + No. of tool users (all time) (usegalaxy.org.au): 18589 + No. of tool users (all time) - all main servers: 83042 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3104 + Tool usage (5 years) (usegalaxy.org): 3693 + Tool usage (5 years) (usegalaxy.org.au): 2467 + Tool usage (5 years) - all main servers: 9264 + Tool usage (all time) (usegalaxy.eu): 3259 + Tool usage (all time) (usegalaxy.org): 3693 + Tool usage (all time) (usegalaxy.org.au): 2650 + Tool usage (all time) - all main servers: 9602 + ToolShed categories: + - Sequence Analysis + ToolShed id: fasta_stats + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: fastani + Conda version: '1.34' + Date of first commit of the suite: '2020-02-17' + Description: Fast alignment-free computation of whole-genome Average Nucleotide + Identity + EDAM operation: + - Genome alignment + - Sequence similarity search + EDAM operation (no superclasses): + - Genome alignment + - Sequence similarity search + EDAM topic: + - Microbiology + - Genetic variation + EDAM topic (no superclasses): + - Microbiology + - Genetic variation + Galaxy tool ids: + - fastani + Galaxy wrapper id: fastani + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani + Galaxy wrapper version: '1.3' + No. of tool users (5 years) (usegalaxy.eu): 6685 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6685 + No. of tool users (all time) (usegalaxy.eu): 6685 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6685 + Source: https://github.com/ParBLiSS/FastANI + Status: To update + Tool usage (5 years) (usegalaxy.eu): 603 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 603 + Tool usage (all time) (usegalaxy.eu): 603 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 603 + ToolShed categories: + - Sequence Analysis + ToolShed id: fastani + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide + identity of orthologous gene pairs shared between two microbial genomes. FastANI + supports pairwise comparison of both complete and draft genome assemblies. + bio.tool id: fastani + bio.tool ids: + - fastani + bio.tool name: FastANI +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: fastk + Conda version: '1.0' + Date of first commit of the suite: '2024-05-03' + Description: 'FastK: A K-mer counter (for HQ assembly data sets)' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastk_fastk + Galaxy wrapper id: fastk + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 136 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 136 + No. of tool users (all time) (usegalaxy.eu): 136 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 136 + Source: https://github.com/thegenemyers/FASTK + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Assembly + ToolShed id: fastk + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastp + Conda version: 0.23.4 + Date of first commit of the suite: '2018-03-18' + Description: Fast all-in-one preprocessing for FASTQ files + EDAM operation: + - Sequencing quality control + - Sequence contamination filtering + EDAM operation (no superclasses): + - Sequence contamination filtering + EDAM topic: + - Sequence analysis + - Probes and primers + EDAM topic (no superclasses): + - Probes and primers + Galaxy tool ids: + - fastp + Galaxy wrapper id: fastp + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp + Galaxy wrapper version: 0.23.4 + No. of tool users (5 years) (usegalaxy.eu): 1126086 + No. of tool users (5 years) (usegalaxy.org): 422259 + No. of tool users (5 years) (usegalaxy.org.au): 76462 + No. of tool users (5 years) - all main servers: 1624807 + No. of tool users (all time) (usegalaxy.eu): 1127111 + No. of tool users (all time) (usegalaxy.org): 422259 + No. of tool users (all time) (usegalaxy.org.au): 76462 + No. of tool users (all time) - all main servers: 1625832 + Source: https://github.com/OpenGene/fastp + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 6847 + Tool usage (5 years) (usegalaxy.org): 10722 + Tool usage (5 years) (usegalaxy.org.au): 2242 + Tool usage (5 years) - all main servers: 19811 + Tool usage (all time) (usegalaxy.eu): 6909 + Tool usage (all time) (usegalaxy.org): 10722 + Tool usage (all time) (usegalaxy.org.au): 2242 + Tool usage (all time) - all main servers: 19873 + ToolShed categories: + - Sequence Analysis + ToolShed id: fastp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 1 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool designed to provide fast all-in-one preprocessing for + FastQ files. This tool is developed in C++ with multithreading supported to afford + high performance. + bio.tool id: fastp + bio.tool ids: + - fastp + bio.tool name: fastp +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastqc + Conda version: 0.12.1 + Date of first commit of the suite: '2017-12-23' + Description: Read QC reports using FastQC + EDAM operation: + - Sequence composition calculation + - Sequencing quality control + - Statistical calculation + EDAM operation (no superclasses): + - Sequence composition calculation + - Sequencing quality control + - Statistical calculation + EDAM topic: + - Sequencing + - Data quality management + - Sequence analysis + EDAM topic (no superclasses): + - Sequencing + - Data quality management + - Sequence analysis + Galaxy tool ids: + - fastqc + Galaxy wrapper id: fastqc + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc + Galaxy wrapper version: 0.74+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 1784056 + No. of tool users (5 years) (usegalaxy.org): 2269843 + No. of tool users (5 years) (usegalaxy.org.au): 410004 + No. of tool users (5 years) - all main servers: 4463903 + No. of tool users (all time) (usegalaxy.eu): 1913280 + No. of tool users (all time) (usegalaxy.org): 3195869 + No. of tool users (all time) (usegalaxy.org.au): 445555 + No. of tool users (all time) - all main servers: 5554704 + Source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 41344 + Tool usage (5 years) (usegalaxy.org): 90828 + Tool usage (5 years) (usegalaxy.org.au): 14195 + Tool usage (5 years) - all main servers: 146367 + Tool usage (all time) (usegalaxy.eu): 43940 + Tool usage (all time) (usegalaxy.org): 140008 + Tool usage (all time) (usegalaxy.org.au): 16026 + Tool usage (all time) - all main servers: 199974 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastqc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 1 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This tool aims to provide a QC report which can spot problems + or biases which originate either in the sequencer or in the starting library material. + It can be run in one of two modes. It can either run as a stand alone interactive + application for the immediate analysis of small numbers of FastQ files, or it + can be run in a non-interactive mode where it would be suitable for integrating + into a larger analysis pipeline for the systematic processing of large numbers + of files. + bio.tool id: fastqc + bio.tool ids: + - fastqc + bio.tool name: FastQC +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastqe + Conda version: 0.3.1 + Date of first commit of the suite: '2020-07-13' + Description: FASTQE + EDAM operation: + - Sequencing quality control + EDAM operation (no superclasses): + - Sequencing quality control + EDAM topic: + - Sequence analysis + - Sequencing + EDAM topic (no superclasses): + - Sequence analysis + - Sequencing + Galaxy tool ids: + - fastqe + Galaxy wrapper id: fastqe + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe + Galaxy wrapper version: 0.3.1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 5162 + No. of tool users (5 years) (usegalaxy.org): 10176 + No. of tool users (5 years) (usegalaxy.org.au): 2610 + No. of tool users (5 years) - all main servers: 17948 + No. of tool users (all time) (usegalaxy.eu): 5162 + No. of tool users (all time) (usegalaxy.org): 10176 + No. of tool users (all time) (usegalaxy.org.au): 2610 + No. of tool users (all time) - all main servers: 17948 + Source: https://fastqe.com/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2350 + Tool usage (5 years) (usegalaxy.org): 4714 + Tool usage (5 years) (usegalaxy.org.au): 991 + Tool usage (5 years) - all main servers: 8055 + Tool usage (all time) (usegalaxy.eu): 2350 + Tool usage (all time) (usegalaxy.org): 4714 + Tool usage (all time) (usegalaxy.org.au): 991 + Tool usage (all time) - all main servers: 8055 + ToolShed categories: + - Sequence Analysis + ToolShed id: fastqe + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Compute quality stats for FASTQ files and print those stats + as emoji... for some reason. + bio.tool id: fastqe + bio.tool ids: + - fastqe + bio.tool name: FASTQE +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fasttree + Conda version: 2.1.11 + Date of first commit of the suite: '2018-02-02' + Description: FastTree infers approximately-maximum-likelihood phylogenetic trees + from alignments of nucleotide or protein sequences - GVL + EDAM operation: + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + EDAM operation (no superclasses): [] + EDAM topic: + - Phylogenetics + - Sequence analysis + EDAM topic (no superclasses): + - Phylogenetics + Galaxy tool ids: + - fasttree + Galaxy wrapper id: fasttree + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree + Galaxy wrapper version: 2.1.10 + No. of tool users (5 years) (usegalaxy.eu): 65542 + No. of tool users (5 years) (usegalaxy.org): 25992 + No. of tool users (5 years) (usegalaxy.org.au): 6733 + No. of tool users (5 years) - all main servers: 98267 + No. of tool users (all time) (usegalaxy.eu): 65631 + No. of tool users (all time) (usegalaxy.org): 25992 + No. of tool users (all time) (usegalaxy.org.au): 7339 + No. of tool users (all time) - all main servers: 98962 + Source: http://www.microbesonline.org/fasttree/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1049 + Tool usage (5 years) (usegalaxy.org): 2147 + Tool usage (5 years) (usegalaxy.org.au): 649 + Tool usage (5 years) - all main servers: 3845 + Tool usage (all time) (usegalaxy.eu): 1071 + Tool usage (all time) (usegalaxy.org): 2147 + Tool usage (all time) (usegalaxy.org.au): 745 + Tool usage (all time) - all main servers: 3963 + ToolShed categories: + - Phylogenetics + ToolShed id: fasttree + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Infers approximately-maximum-likelihood phylogenetic trees + from alignments of nucleotide or protein sequences. + bio.tool id: fasttree + bio.tool ids: + - fasttree + bio.tool name: FastTree +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: subread + Conda version: 2.0.6 + Date of first commit of the suite: '2019-05-28' + Description: featureCounts counts the number of reads aligned to defined masked + regions in a reference genome + EDAM operation: + - Read summarisation + - RNA-Seq quantification + EDAM operation (no superclasses): + - Read summarisation + - RNA-Seq quantification + EDAM topic: + - RNA-Seq + EDAM topic (no superclasses): + - RNA-Seq + Galaxy tool ids: + - featurecounts + Galaxy wrapper id: featurecounts + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts + Galaxy wrapper version: 2.0.3 + No. of tool users (5 years) (usegalaxy.eu): 740719 + No. of tool users (5 years) (usegalaxy.org): 643892 + No. of tool users (5 years) (usegalaxy.org.au): 66108 + No. of tool users (5 years) - all main servers: 1450719 + No. of tool users (all time) (usegalaxy.eu): 770524 + No. of tool users (all time) (usegalaxy.org): 784396 + No. of tool users (all time) (usegalaxy.org.au): 68867 + No. of tool users (all time) - all main servers: 1623787 + Source: http://bioinf.wehi.edu.au/featureCounts + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11699 + Tool usage (5 years) (usegalaxy.org): 23272 + Tool usage (5 years) (usegalaxy.org.au): 2348 + Tool usage (5 years) - all main servers: 37319 + Tool usage (all time) (usegalaxy.eu): 12547 + Tool usage (all time) (usegalaxy.org): 27598 + Tool usage (all time) (usegalaxy.org.au): 2463 + Tool usage (all time) - all main servers: 42608 + ToolShed categories: + - RNA + - Transcriptomics + - Sequence Analysis + ToolShed id: featurecounts + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: featureCounts is a very efficient read quantifier. It can + be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic + features such as genes, exons, promoters, gene bodies and genomic bins. It is + included in the Bioconductor Rsubread package and also in the SourceForge Subread + package. + bio.tool id: featurecounts + bio.tool ids: + - featurecounts + bio.tool name: FeatureCounts +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: feelnc + Conda version: '0.2' + Date of first commit of the suite: '2018-03-27' + Description: Galaxy wrapper for FEELnc + EDAM operation: + - Annotation + - Classification + EDAM operation (no superclasses): + - Annotation + - Classification + EDAM topic: + - RNA-seq + - Functional, regulatory and non-coding RNA + EDAM topic (no superclasses): + - Functional, regulatory and non-coding RNA + Galaxy tool ids: + - feelnc + Galaxy wrapper id: feelnc + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc + Galaxy wrapper version: 0.2.1 + No. of tool users (5 years) (usegalaxy.eu): 1375 + No. of tool users (5 years) (usegalaxy.org): 797 + No. of tool users (5 years) (usegalaxy.org.au): 59 + No. of tool users (5 years) - all main servers: 2231 + No. of tool users (all time) (usegalaxy.eu): 1500 + No. of tool users (all time) (usegalaxy.org): 797 + No. of tool users (all time) (usegalaxy.org.au): 59 + No. of tool users (all time) - all main servers: 2356 + Source: https://github.com/tderrien/FEELnc + Status: To update + Tool usage (5 years) (usegalaxy.eu): 95 + Tool usage (5 years) (usegalaxy.org): 116 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 214 + Tool usage (all time) (usegalaxy.eu): 99 + Tool usage (all time) (usegalaxy.org): 116 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 218 + ToolShed categories: + - Sequence Analysis + ToolShed id: feelnc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool to annotate long non-coding RNAs from RNA-seq assembled + transcripts. + bio.tool id: feelnc + bio.tool ids: + - feelnc + bio.tool name: FEELnc +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: fermi2 + Conda version: r193 + Date of first commit of the suite: '2017-01-05' + Description: FermiKit is a de novo assembly based variant calling pipeline for deep + Illumina resequencing data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fermi2 + - fermikit_variants + Galaxy wrapper id: fermikit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit + Galaxy wrapper version: r193 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/lh3/fermikit + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + - Variant Analysis + ToolShed id: fermikit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-fgsea + Conda version: 1.28.0 + Date of first commit of the suite: '2018-10-19' + Description: Perform gene set testing using fgsea + EDAM operation: + - Gene-set enrichment analysis + EDAM operation (no superclasses): + - Gene-set enrichment analysis + EDAM topic: + - Genetics + EDAM topic (no superclasses): + - Genetics + Galaxy tool ids: + - fgsea + Galaxy wrapper id: fgsea + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea + Galaxy wrapper version: 1.8.0+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 5618 + No. of tool users (5 years) (usegalaxy.org): 21673 + No. of tool users (5 years) (usegalaxy.org.au): 869 + No. of tool users (5 years) - all main servers: 28160 + No. of tool users (all time) (usegalaxy.eu): 5820 + No. of tool users (all time) (usegalaxy.org): 21673 + No. of tool users (all time) (usegalaxy.org.au): 869 + No. of tool users (all time) - all main servers: 28362 + Source: https://bioconductor.org/packages/release/bioc/html/fgsea.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 582 + Tool usage (5 years) (usegalaxy.org): 938 + Tool usage (5 years) (usegalaxy.org.au): 110 + Tool usage (5 years) - all main servers: 1630 + Tool usage (all time) (usegalaxy.eu): 607 + Tool usage (all time) (usegalaxy.org): 938 + Tool usage (all time) (usegalaxy.org.au): 110 + Tool usage (all time) - all main servers: 1655 + ToolShed categories: + - Visualization + - Transcriptomics + - Statistics + ToolShed id: fgsea + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: The package implements an algorithm for fast gene set enrichment + analysis. Using the fast algorithm allows to make more permutations and get more + fine grained p-values, which allows to use accurate stantard approaches to multiple + hypothesis correction. + bio.tool id: fgsea + bio.tool ids: + - fgsea + bio.tool name: fgsea +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: filtlong + Conda version: 0.2.1 + Date of first commit of the suite: '2018-09-14' + Description: Filtlong - Filtering long reads by quality + EDAM operation: + - Filtering + - Sequencing quality control + EDAM operation (no superclasses): + - Filtering + - Sequencing quality control + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - filtlong + Galaxy wrapper id: filtlong + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong + Galaxy wrapper version: 0.2.1 + No. of tool users (5 years) (usegalaxy.eu): 53310 + No. of tool users (5 years) (usegalaxy.org): 25043 + No. of tool users (5 years) (usegalaxy.org.au): 10824 + No. of tool users (5 years) - all main servers: 89177 + No. of tool users (all time) (usegalaxy.eu): 53944 + No. of tool users (all time) (usegalaxy.org): 25043 + No. of tool users (all time) (usegalaxy.org.au): 10824 + No. of tool users (all time) - all main servers: 89811 + Source: https://github.com/rrwick/Filtlong + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1499 + Tool usage (5 years) (usegalaxy.org): 726 + Tool usage (5 years) (usegalaxy.org.au): 593 + Tool usage (5 years) - all main servers: 2818 + Tool usage (all time) (usegalaxy.eu): 1575 + Tool usage (all time) (usegalaxy.org): 726 + Tool usage (all time) (usegalaxy.org.au): 593 + Tool usage (all time) - all main servers: 2894 + ToolShed categories: + - Fastq Manipulation + - Sequence Analysis + ToolShed id: filtlong + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Filtlong is a tool for filtering long reads by quality. It + can take a set of long reads and produce a smaller, better subset. It uses both + read length (longer is better) and read identity (higher is better) when choosing + which reads pass the filter. + bio.tool id: filtlong + bio.tool ids: + - filtlong + bio.tool name: Filtlong +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: flair + Conda version: 2.0.0 + Date of first commit of the suite: '2020-11-19' + Description: FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, + isoform definition, and alternative splicing analysis of noisy reads. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - flair_collapse + - flair_correct + Galaxy wrapper id: flair + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair + Galaxy wrapper version: '1.5' + No. of tool users (5 years) (usegalaxy.eu): 1985 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1985 + No. of tool users (all time) (usegalaxy.eu): 1985 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1985 + Source: https://github.com/BrooksLabUCSC/flair + Status: To update + Tool usage (5 years) (usegalaxy.eu): 41 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 41 + Tool usage (all time) (usegalaxy.eu): 41 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 41 + ToolShed categories: + - Nanopore + ToolShed id: flair + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: flash + Conda version: 1.2.11 + Date of first commit of the suite: '2017-09-25' + Description: Fast Length Adjustment of SHort reads + EDAM operation: + - Read pre-processing + - Sequence merging + - Sequence assembly + EDAM operation (no superclasses): + - Read pre-processing + - Sequence merging + - Sequence assembly + EDAM topic: + - Sequencing + - Sequence assembly + EDAM topic (no superclasses): + - Sequencing + - Sequence assembly + Galaxy tool ids: + - flash + Galaxy wrapper id: flash + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash + Galaxy wrapper version: 1.2.11 + No. of tool users (5 years) (usegalaxy.eu): 22017 + No. of tool users (5 years) (usegalaxy.org): 9399 + No. of tool users (5 years) (usegalaxy.org.au): 4 + No. of tool users (5 years) - all main servers: 31420 + No. of tool users (all time) (usegalaxy.eu): 22304 + No. of tool users (all time) (usegalaxy.org): 14886 + No. of tool users (all time) (usegalaxy.org.au): 4 + No. of tool users (all time) - all main servers: 37194 + Source: https://ccb.jhu.edu/software/FLASH/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 239 + Tool usage (5 years) (usegalaxy.org): 462 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 702 + Tool usage (all time) (usegalaxy.eu): 255 + Tool usage (all time) (usegalaxy.org): 709 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 965 + ToolShed categories: + - Assembly + - Fastq Manipulation + ToolShed id: flash + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Identifies paired-end reads which overlap in the middle, converting + them to single long reads + bio.tool id: flash + bio.tool ids: + - flash + bio.tool name: FLASH +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: fraggenescan + Conda version: '1.31' + Date of first commit of the suite: '2017-09-04' + Description: Tool for finding (fragmented) genes in short read + EDAM operation: + - Gene prediction + EDAM operation (no superclasses): + - Gene prediction + EDAM topic: + - Genetics + - Sequence analysis + EDAM topic (no superclasses): + - Genetics + - Sequence analysis + Galaxy tool ids: + - fraggenescan + Galaxy wrapper id: fraggenescan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 1257 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1052 + No. of tool users (5 years) - all main servers: 2309 + No. of tool users (all time) (usegalaxy.eu): 1450 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1052 + No. of tool users (all time) - all main servers: 2502 + Source: https://sourceforge.net/projects/fraggenescan/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 150 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 45 + Tool usage (5 years) - all main servers: 195 + Tool usage (all time) (usegalaxy.eu): 162 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 45 + Tool usage (all time) - all main servers: 207 + ToolShed categories: + - Sequence Analysis + ToolShed id: fraggenescan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Application for finding (fragmented) genes in short reads + bio.tool id: fraggenescan + bio.tool ids: + - fraggenescan + bio.tool name: FragGeneScan +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: freebayes + Conda version: 1.3.8 + Date of first commit of the suite: '2017-01-23' + Description: Galaxy Freebayes Bayesian genetic variant detector tool + EDAM operation: + - Variant calling + - Statistical calculation + EDAM operation (no superclasses): + - Variant calling + - Statistical calculation + EDAM topic: + - Genomics + - Genetic variation + - Rare diseases + EDAM topic (no superclasses): + - Genomics + - Genetic variation + - Rare diseases + Galaxy tool ids: + - freebayes + - bamleftalign + Galaxy wrapper id: freebayes + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes + Galaxy wrapper version: 1.3.8 + No. of tool users (5 years) (usegalaxy.eu): 149715 + No. of tool users (5 years) (usegalaxy.org): 144708 + No. of tool users (5 years) (usegalaxy.org.au): 19156 + No. of tool users (5 years) - all main servers: 313579 + No. of tool users (all time) (usegalaxy.eu): 171093 + No. of tool users (all time) (usegalaxy.org): 256315 + No. of tool users (all time) (usegalaxy.org.au): 21936 + No. of tool users (all time) - all main servers: 449344 + Source: https://github.com/ekg/freebayes + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 8158 + Tool usage (5 years) (usegalaxy.org): 15996 + Tool usage (5 years) (usegalaxy.org.au): 2251 + Tool usage (5 years) - all main servers: 26405 + Tool usage (all time) (usegalaxy.eu): 8794 + Tool usage (all time) (usegalaxy.org): 25107 + Tool usage (all time) (usegalaxy.org.au): 2571 + Tool usage (all time) - all main servers: 36472 + ToolShed categories: + - Variant Analysis + ToolShed id: freebayes + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Bayesian genetic variant detector designed to find small polymorphisms, + specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events + (composite insertion and substitution events) smaller than the length of a short-read + sequencing alignment. + bio.tool id: freebayes + bio.tool ids: + - freebayes + bio.tool name: FreeBayes +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: gawk + Conda version: null + Date of first commit of the suite: '2020-08-13' + Description: Control-FREEC is a tool for detection of copy-number changes and allelic + imbalances (including LOH) using deep-sequencing data originally developed by + the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, + normalizes, segments copy number and beta allele frequency (BAF) profiles, then + calls copy number alterations and LOH. + EDAM operation: + - Copy number estimation + - Variant calling + - Genome alignment + EDAM operation (no superclasses): + - Copy number estimation + - Variant calling + - Genome alignment + EDAM topic: + - DNA structural variation + - Oncology + - Human genetics + - Data mining + EDAM topic (no superclasses): + - Oncology + - Human genetics + - Data mining + Galaxy tool ids: + - control_freec + Galaxy wrapper id: freec + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec + Galaxy wrapper version: '11.6' + No. of tool users (5 years) (usegalaxy.eu): 748 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 12 + No. of tool users (5 years) - all main servers: 760 + No. of tool users (all time) (usegalaxy.eu): 748 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 12 + No. of tool users (all time) - all main servers: 760 + Source: http://boevalab.inf.ethz.ch/FREEC/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 91 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 92 + Tool usage (all time) (usegalaxy.eu): 91 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 92 + ToolShed categories: + - Variant Analysis + ToolShed id: control_freec + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool for control-free copy number alteration (CNA) and allelic + imbalances (LOH) detection using deep-sequencing data, particularly useful for + cancer studies. + bio.tool id: freec + bio.tool ids: + - freec + bio.tool name: FREEC +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: freyja + Conda version: 1.5.1 + Date of first commit of the suite: '2022-07-05' + Description: lineage abundances estimation + EDAM operation: + - RNA-Seq quantification + EDAM operation (no superclasses): + - RNA-Seq quantification + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - freyja_aggregate_plot + - freyja_boot + - freyja_demix + - freyja_variants + Galaxy wrapper id: freyja + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja + Galaxy wrapper version: 1.5.1 + No. of tool users (5 years) (usegalaxy.eu): 21757 + No. of tool users (5 years) (usegalaxy.org): 217 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 21974 + No. of tool users (all time) (usegalaxy.eu): 21757 + No. of tool users (all time) (usegalaxy.org): 217 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 21974 + Source: https://github.com/andersen-lab/Freyja + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 101 + Tool usage (5 years) (usegalaxy.org): 21 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 122 + Tool usage (all time) (usegalaxy.eu): 101 + Tool usage (all time) (usegalaxy.org): 21 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 122 + ToolShed categories: + - Metagenomics + - Sequence Analysis + ToolShed id: freyja + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 4 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 4 + UseGalaxy.or: 2 + biii: null + bio.tool description: Recover relative lineage abundances from mixed SARS-CoV-2 + samples from a sequencing dataset + bio.tool id: freyja + bio.tool ids: + - freyja + bio.tool name: Freyja +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 0 + Conda id: matplotlib + Conda version: null + Date of first commit of the suite: '2019-10-24' + Description: Tool that plots a histogram of sizes of read families + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fsd + - fsd_beforevsafter + - fsd_regions + - td + Galaxy wrapper id: fsd + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 578 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 578 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 578 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 578 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 34 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 34 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 34 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 34 + ToolShed categories: + - Graphics + ToolShed id: duplex_family_size_distribution + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 5 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-08-26' + Description: Funannotate is a genome prediction, annotation, and comparison software + package. + EDAM operation: + - Genome annotation + EDAM operation (no superclasses): + - Genome annotation + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - funannotate_annotate + - funannotate_clean + - funannotate_compare + - funannotate_predict + - funannotate_sort + Galaxy wrapper id: funannotate + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate + Galaxy wrapper version: 1.8.15 + No. of tool users (5 years) (usegalaxy.eu): 8648 + No. of tool users (5 years) (usegalaxy.org): 32 + No. of tool users (5 years) (usegalaxy.org.au): 6406 + No. of tool users (5 years) - all main servers: 15086 + No. of tool users (all time) (usegalaxy.eu): 8648 + No. of tool users (all time) (usegalaxy.org): 32 + No. of tool users (all time) (usegalaxy.org.au): 6406 + No. of tool users (all time) - all main servers: 15086 + Source: https://funannotate.readthedocs.io + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1408 + Tool usage (5 years) (usegalaxy.org): 6 + Tool usage (5 years) (usegalaxy.org.au): 597 + Tool usage (5 years) - all main servers: 2011 + Tool usage (all time) (usegalaxy.eu): 1408 + Tool usage (all time) (usegalaxy.org): 6 + Tool usage (all time) (usegalaxy.org.au): 597 + Tool usage (all time) - all main servers: 2011 + ToolShed categories: + - Genome annotation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: funannotate is a pipeline for genome annotation (built specifically + for fungi, but will also work with higher eukaryotes). + bio.tool id: funannotate + bio.tool ids: + - funannotate + bio.tool name: funannotate +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: gatk4 + Conda version: 4.5.0.0 + Date of first commit of the suite: '2019-10-28' + Description: A Galaxy wrapper for Mutect2 from GATK + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gatk4_mutect2 + Galaxy wrapper id: gatk4 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 + Galaxy wrapper version: 4.1.7.0 + No. of tool users (5 years) (usegalaxy.eu): 3463 + No. of tool users (5 years) (usegalaxy.org): 9040 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 12503 + No. of tool users (all time) (usegalaxy.eu): 3463 + No. of tool users (all time) (usegalaxy.org): 9040 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 12503 + Source: https://software.broadinstitute.org/gatk/gatk4 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 452 + Tool usage (5 years) (usegalaxy.org): 1639 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2091 + Tool usage (all time) (usegalaxy.eu): 452 + Tool usage (all time) (usegalaxy.org): 1639 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2091 + ToolShed categories: + - Variant Analysis + ToolShed id: gatk4_mutect2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2017-06-23' + Description: GDCWebApp automatically filter, extract, and convert genomic data from + the Genomic Data Commons portal to BED format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - data_source_gdcwebapp + Galaxy wrapper id: gdcwebapp + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp + Galaxy wrapper source: https://github.com/fabio-cumbo/GDCWebApp4Galaxy + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://bioinf.iasi.cnr.it/gdcwebapp/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Data Source + - Convert Formats + ToolShed id: gdcwebapp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: gecko + Conda version: '1.2' + Date of first commit of the suite: '2020-11-25' + Description: Ungapped genome comparison + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gecko + Galaxy wrapper id: gecko + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko + Galaxy wrapper version: '1.2' + No. of tool users (5 years) (usegalaxy.eu): 723 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 786 + No. of tool users (5 years) - all main servers: 1509 + No. of tool users (all time) (usegalaxy.eu): 723 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 786 + No. of tool users (all time) - all main servers: 1509 + Source: https://github.com/otorreno/gecko + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 235 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 95 + Tool usage (5 years) - all main servers: 330 + Tool usage (all time) (usegalaxy.eu): 235 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 95 + Tool usage (all time) - all main servers: 330 + ToolShed categories: + - Sequence Analysis + ToolShed id: gecko + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 2 + Conda id: gemini + Conda version: 0.30.2 + Date of first commit of the suite: '2019-01-05' + Description: 'GEMINI: a flexible framework for exploring genome variation' + EDAM operation: + - Sequence analysis + - Genetic variation analysis + EDAM operation (no superclasses): + - Sequence analysis + - Genetic variation analysis + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_db_info + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_inheritance + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + - gemini_@BINARY@ + Galaxy wrapper id: gemini + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini + Galaxy wrapper version: 0.20.1 + No. of tool users (5 years) (usegalaxy.eu): 4967 + No. of tool users (5 years) (usegalaxy.org): 992 + No. of tool users (5 years) (usegalaxy.org.au): 3756 + No. of tool users (5 years) - all main servers: 9715 + No. of tool users (all time) (usegalaxy.eu): 5475 + No. of tool users (all time) (usegalaxy.org): 1118 + No. of tool users (all time) (usegalaxy.org.au): 3811 + No. of tool users (all time) - all main servers: 10404 + Source: https://github.com/arq5x/gemini + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1863 + Tool usage (5 years) (usegalaxy.org): 279 + Tool usage (5 years) (usegalaxy.org.au): 423 + Tool usage (5 years) - all main servers: 2565 + Tool usage (all time) (usegalaxy.eu): 1992 + Tool usage (all time) (usegalaxy.org): 370 + Tool usage (all time) (usegalaxy.org.au): 425 + Tool usage (all time) - all main servers: 2787 + ToolShed categories: + - Sequence Analysis + - Next Gen Mappers + ToolShed id: gemini + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: GEMINI (GEnome MINIng) is a flexible framework for exploring + genetic variation in the context of the wealth of genome annotations available + for the human genome. By placing genetic variants, sample phenotypes and genotypes, + as well as genome annotations into an integrated database framework, GEMINI provides + a simple, flexible, and powerful system for exploring genetic variation for disease + and population genetics. + bio.tool id: gemini + bio.tool ids: + - gemini + bio.tool name: GEMINI +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-08-05' + Description: Stitch gene blocks given a set of coding exon intervals + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - GeneBed_Maf_Fasta2 + Galaxy wrapper id: genebed_maf_to_fasta + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ + Galaxy wrapper version: 1.0.1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 4 + No. of tool users (5 years) (usegalaxy.org): 221 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 225 + No. of tool users (all time) (usegalaxy.eu): 4 + No. of tool users (all time) (usegalaxy.org): 2905 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2909 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 23 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 25 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 279 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 281 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: genebed_maf_to_fasta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 1 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 1 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 1 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ghm + Conda version: '3.1' + Date of first commit of the suite: '2017-11-27' + Description: Maximised LOD score pedigree analysis utility + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - genehunter_modscore + Galaxy wrapper id: genehunter_modscore + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ + Galaxy wrapper version: 3.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: genehunter_modscore + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-06-20' + Description: Gene.iobio is an interactive tool for variant and trio analysis. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gene_iobio_display_generation_iframe + Galaxy wrapper id: geneiobio + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio + Galaxy wrapper version: 4.7.1+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 101 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 59 + No. of tool users (5 years) - all main servers: 160 + No. of tool users (all time) (usegalaxy.eu): 101 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 59 + No. of tool users (all time) - all main servers: 160 + Source: https://github.com/iobio/gene.iobio + Status: To update + Tool usage (5 years) (usegalaxy.eu): 25 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 6 + Tool usage (5 years) - all main servers: 31 + Tool usage (all time) (usegalaxy.eu): 25 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 6 + Tool usage (all time) - all main servers: 31 + ToolShed categories: + - Sequence Analysis + ToolShed id: geneiobio + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2015-12-18' + Description: "Contains a tool that separately identifies peaks on the forward \"\ + +\u201D (W) and reverse \u201C-\u201D (C) strand." + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - genetrack + Galaxy wrapper id: genetrack + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 445 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 445 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 660 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 660 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 104 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 104 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 197 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 197 + ToolShed categories: + - ChIP-seq + ToolShed id: genetrack + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: genomescope2 + Conda version: 2.0.1 + Date of first commit of the suite: '2021-04-30' + Description: Analyze unassembled short reads + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - genomescope + Galaxy wrapper id: genomescope + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope + Galaxy wrapper version: 2.0.1 + No. of tool users (5 years) (usegalaxy.eu): 3181 + No. of tool users (5 years) (usegalaxy.org): 2112 + No. of tool users (5 years) (usegalaxy.org.au): 1622 + No. of tool users (5 years) - all main servers: 6915 + No. of tool users (all time) (usegalaxy.eu): 3181 + No. of tool users (all time) (usegalaxy.org): 2112 + No. of tool users (all time) (usegalaxy.org.au): 1622 + No. of tool users (all time) - all main servers: 6915 + Source: https://github.com/tbenavi1/genomescope2.0 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 665 + Tool usage (5 years) (usegalaxy.org): 435 + Tool usage (5 years) (usegalaxy.org.au): 148 + Tool usage (5 years) - all main servers: 1248 + Tool usage (all time) (usegalaxy.eu): 665 + Tool usage (all time) (usegalaxy.org): 435 + Tool usage (all time) (usegalaxy.org.au): 148 + Tool usage (all time) - all main servers: 1248 + ToolShed categories: + - Statistics + ToolShed id: genomescope + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-genomicsupersignature + Conda version: 1.10.0 + Date of first commit of the suite: '2022-01-12' + Description: Interpretation of RNAseq experiments through robust, efficient comparison + to public databases + EDAM operation: + - Gene-set enrichment analysis + - Essential dynamics + - Deposition + - Principal component visualisation + - Dimensionality reduction + EDAM operation (no superclasses): + - Gene-set enrichment analysis + - Essential dynamics + - Deposition + - Principal component visualisation + - Dimensionality reduction + EDAM topic: + - RNA-Seq + - Transcriptomics + - Microbial ecology + - Genotype and phenotype + - Microarray experiment + EDAM topic (no superclasses): + - RNA-Seq + - Transcriptomics + - Microbial ecology + - Genotype and phenotype + - Microarray experiment + Galaxy tool ids: + - genomic_super_signature + Galaxy wrapper id: genomic_super_signature + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 47 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 47 + No. of tool users (all time) (usegalaxy.eu): 47 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 47 + Source: https://github.com/shbrief/GenomicSuperSignature + Status: To update + Tool usage (5 years) (usegalaxy.eu): 13 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 13 + Tool usage (all time) (usegalaxy.eu): 13 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 13 + ToolShed categories: + - Sequence Analysis + - RNA + - Transcriptomics + ToolShed id: genomic_super_signature + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: GenomicSuperSignature is a package for the interpretation + of RNA-seq experiments through robust, efficient comparison to public databases. + bio.tool id: genomicsupersignature + bio.tool ids: + - genomicsupersignature + bio.tool name: GenomicSuperSignature +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: genrich + Conda version: 0.6.1 + Date of first commit of the suite: '2019-07-05' + Description: Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, + ATAC-seq). + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - genrich + Galaxy wrapper id: genrich + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich + Galaxy wrapper source: https://github.com/jsh58/Genrich + Galaxy wrapper version: 0.5+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 3534 + No. of tool users (5 years) (usegalaxy.org): 2840 + No. of tool users (5 years) (usegalaxy.org.au): 571 + No. of tool users (5 years) - all main servers: 6945 + No. of tool users (all time) (usegalaxy.eu): 3577 + No. of tool users (all time) (usegalaxy.org): 2840 + No. of tool users (all time) (usegalaxy.org.au): 571 + No. of tool users (all time) - all main servers: 6988 + Source: https://github.com/jsh58/Genrich + Status: To update + Tool usage (5 years) (usegalaxy.eu): 402 + Tool usage (5 years) (usegalaxy.org): 419 + Tool usage (5 years) (usegalaxy.org.au): 31 + Tool usage (5 years) - all main servers: 852 + Tool usage (all time) (usegalaxy.eu): 405 + Tool usage (all time) (usegalaxy.org): 419 + Tool usage (all time) (usegalaxy.org.au): 31 + Tool usage (all time) - all main servers: 855 + ToolShed categories: + - ChIP-seq + ToolShed id: genrich + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pyfaidx + Conda version: 0.8.1.3 + Date of first commit of the suite: '2021-03-02' + Description: Annotate indel variants with homopolymer context + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - get_hrun + Galaxy wrapper id: get_hrun + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun + Galaxy wrapper version: 0.5.9.2 + No. of tool users (5 years) (usegalaxy.eu): 9 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 9 + No. of tool users (all time) (usegalaxy.eu): 9 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 9 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Variant Analysis + ToolShed id: get_hrun + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 2 + Conda id: getorganelle + Conda version: 1.7.7.1 + Date of first commit of the suite: '2022-05-04' + Description: GetOrganelle - This toolkit assembles organelle genomes from genomic + skimming data. + EDAM operation: + - De-novo assembly + - Genome assembly + - Mapping assembly + - Mapping + - Sequence trimming + EDAM operation (no superclasses): + - De-novo assembly + - Genome assembly + - Mapping assembly + - Mapping + - Sequence trimming + EDAM topic: + - Cell biology + - Sequence assembly + - Whole genome sequencing + - Plant biology + - Model organisms + EDAM topic (no superclasses): + - Cell biology + - Sequence assembly + - Whole genome sequencing + - Plant biology + - Model organisms + Galaxy tool ids: + - get_annotated_regions_from_gb + - get_organelle_from_reads + Galaxy wrapper id: getorganelle + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle + Galaxy wrapper version: 1.7.7.1 + No. of tool users (5 years) (usegalaxy.eu): 1542 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 587 + No. of tool users (5 years) - all main servers: 2129 + No. of tool users (all time) (usegalaxy.eu): 1542 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 587 + No. of tool users (all time) - all main servers: 2129 + Source: https://github.com/Kinggerm/GetOrganelle + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 159 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 64 + Tool usage (5 years) - all main servers: 223 + Tool usage (all time) (usegalaxy.eu): 159 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 64 + Tool usage (all time) - all main servers: 223 + ToolShed categories: + - Assembly + ToolShed id: getorganelle + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: A fast and versatile toolkit for accurate de novo assembly + of organelle genomes.This toolkit assemblies organelle genome from genomic skimming + data. + bio.tool id: getorganelle + bio.tool ids: + - getorganelle + bio.tool name: GetOrganelle +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2019-06-18' + Description: gfa_to_fa - Converting GFA format to Fasta format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gfa_to_fa + Galaxy wrapper id: gfa_to_fa + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 9664 + No. of tool users (5 years) (usegalaxy.org): 5623 + No. of tool users (5 years) (usegalaxy.org.au): 1000 + No. of tool users (5 years) - all main servers: 16287 + No. of tool users (all time) (usegalaxy.eu): 9775 + No. of tool users (all time) (usegalaxy.org): 5623 + No. of tool users (all time) (usegalaxy.org.au): 1000 + No. of tool users (all time) - all main servers: 16398 + Source: http://gfa-spec.github.io/GFA-spec/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 763 + Tool usage (5 years) (usegalaxy.org): 493 + Tool usage (5 years) (usegalaxy.org.au): 135 + Tool usage (5 years) - all main servers: 1391 + Tool usage (all time) (usegalaxy.eu): 765 + Tool usage (all time) (usegalaxy.org): 493 + Tool usage (all time) (usegalaxy.org.au): 135 + Tool usage (all time) - all main servers: 1393 + ToolShed categories: + - Convert Formats + ToolShed id: gfa_to_fa + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bcbiogff + Conda version: 0.6.6 + Date of first commit of the suite: '2015-05-25' + Description: Rebase a GFF against a parent GFF (e.g. an original genome) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gff3.rebase + Galaxy wrapper id: gff3_rebase + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase + Galaxy wrapper version: '1.2' + No. of tool users (5 years) (usegalaxy.eu): 806 + No. of tool users (5 years) (usegalaxy.org): 197 + No. of tool users (5 years) (usegalaxy.org.au): 132 + No. of tool users (5 years) - all main servers: 1135 + No. of tool users (all time) (usegalaxy.eu): 812 + No. of tool users (all time) (usegalaxy.org): 197 + No. of tool users (all time) (usegalaxy.org.au): 132 + No. of tool users (all time) - all main servers: 1141 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase + Status: To update + Tool usage (5 years) (usegalaxy.eu): 68 + Tool usage (5 years) (usegalaxy.org): 37 + Tool usage (5 years) (usegalaxy.org.au): 12 + Tool usage (5 years) - all main servers: 117 + Tool usage (all time) (usegalaxy.eu): 68 + Tool usage (all time) (usegalaxy.org): 37 + Tool usage (all time) (usegalaxy.org.au): 12 + Tool usage (all time) - all main servers: 117 + ToolShed categories: + - Sequence Analysis + ToolShed id: gff3_rebase + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: gffcompare + Conda version: 0.12.6 + Date of first commit of the suite: '2018-10-29' + Description: Galaxy wrappers for Geo Pertea's GffCompare package. + EDAM operation: + - Sequence annotation + EDAM operation (no superclasses): + - Sequence annotation + EDAM topic: + - Nucleic acids + - Sequence analysis + EDAM topic (no superclasses): + - Nucleic acids + - Sequence analysis + Galaxy tool ids: + - gffcompare + Galaxy wrapper id: gffcompare + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare + Galaxy wrapper version: 0.12.6 + No. of tool users (5 years) (usegalaxy.eu): 3560 + No. of tool users (5 years) (usegalaxy.org): 5281 + No. of tool users (5 years) (usegalaxy.org.au): 1468 + No. of tool users (5 years) - all main servers: 10309 + No. of tool users (all time) (usegalaxy.eu): 3980 + No. of tool users (all time) (usegalaxy.org): 8000 + No. of tool users (all time) (usegalaxy.org.au): 1642 + No. of tool users (all time) - all main servers: 13622 + Source: https://github.com/gpertea/gffcompare/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 916 + Tool usage (5 years) (usegalaxy.org): 1713 + Tool usage (5 years) (usegalaxy.org.au): 208 + Tool usage (5 years) - all main servers: 2837 + Tool usage (all time) (usegalaxy.eu): 999 + Tool usage (all time) (usegalaxy.org): 2521 + Tool usage (all time) (usegalaxy.org.au): 225 + Tool usage (all time) - all main servers: 3745 + ToolShed categories: + - Transcriptomics + ToolShed id: gffcompare + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Program for comparing, annotating, merging and tracking transcripts + in GFF files. + bio.tool id: gffcompare + bio.tool ids: + - gffcompare + bio.tool name: gffcompare +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: gffread + Conda version: 0.12.7 + Date of first commit of the suite: '2019-10-29' + Description: gffread filters and/or converts GFF3/GTF2 records + EDAM operation: + - Sequence annotation + EDAM operation (no superclasses): + - Sequence annotation + EDAM topic: + - Nucleic acids + - Sequence analysis + EDAM topic (no superclasses): + - Nucleic acids + - Sequence analysis + Galaxy tool ids: + - gffread + Galaxy wrapper id: gffread + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread + Galaxy wrapper version: 0.12.7 + No. of tool users (5 years) (usegalaxy.eu): 12828 + No. of tool users (5 years) (usegalaxy.org): 15217 + No. of tool users (5 years) (usegalaxy.org.au): 4423 + No. of tool users (5 years) - all main servers: 32468 + No. of tool users (all time) (usegalaxy.eu): 13716 + No. of tool users (all time) (usegalaxy.org): 23818 + No. of tool users (all time) (usegalaxy.org.au): 4423 + No. of tool users (all time) - all main servers: 41957 + Source: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1740 + Tool usage (5 years) (usegalaxy.org): 2588 + Tool usage (5 years) (usegalaxy.org.au): 732 + Tool usage (5 years) - all main servers: 5060 + Tool usage (all time) (usegalaxy.eu): 1829 + Tool usage (all time) (usegalaxy.org): 3486 + Tool usage (all time) (usegalaxy.org.au): 732 + Tool usage (all time) - all main servers: 6047 + ToolShed categories: + - Sequence Analysis + ToolShed id: gffread + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: program for filtering, converting and manipulating GFF files + bio.tool id: gffread + bio.tool ids: + - gffread + bio.tool name: gffread +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2018-04-26' + Description: ggplot2 is a system for declaratively creating graphics, based on The + Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to + aesthetics, what graphical primitives to use,and it takes care of the details. + EDAM operation: + - Visualisation + EDAM operation (no superclasses): + - Visualisation + EDAM topic: + - Data visualisation + EDAM topic (no superclasses): + - Data visualisation + Galaxy tool ids: + - ggplot2_heatmap + - ggplot2_pca + - ggplot2_histogram + - ggplot2_point + - ggplot2_violin + Galaxy wrapper id: ggplot2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 + Galaxy wrapper version: 3.4.0 + No. of tool users (5 years) (usegalaxy.eu): 24606 + No. of tool users (5 years) (usegalaxy.org): 26805 + No. of tool users (5 years) (usegalaxy.org.au): 8174 + No. of tool users (5 years) - all main servers: 59585 + No. of tool users (all time) (usegalaxy.eu): 25662 + No. of tool users (all time) (usegalaxy.org): 26808 + No. of tool users (all time) (usegalaxy.org.au): 8237 + No. of tool users (all time) - all main servers: 60707 + Source: https://github.com/tidyverse/ggplot2 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3463 + Tool usage (5 years) (usegalaxy.org): 5143 + Tool usage (5 years) (usegalaxy.org.au): 1259 + Tool usage (5 years) - all main servers: 9865 + Tool usage (all time) (usegalaxy.eu): 3630 + Tool usage (all time) (usegalaxy.org): 5144 + Tool usage (all time) (usegalaxy.org.au): 1279 + Tool usage (all time) - all main servers: 10053 + ToolShed categories: + - Visualization + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 5 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 3 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 3 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: Plotting system for R, based on the grammar of graphics. + bio.tool id: ggplot2 + bio.tool ids: + - ggplot2 + bio.tool name: ggplot2 +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-ggupset + Conda version: null + Date of first commit of the suite: '2022-12-17' + Description: Create Upset Plots with ggupset + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - emc-ggupset + Galaxy wrapper id: ggupset + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/const-ae/ggupset + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Graphics + ToolShed id: ggupset + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: glimmer + Conda version: '3.02' + Date of first commit of the suite: '2017-11-28' + Description: Glimmer makes gene predictions. + EDAM operation: + - Sequence analysis + - Genetic variation analysis + EDAM operation (no superclasses): + - Sequence analysis + - Genetic variation analysis + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - glimmer_acgt_content + - glimmer_build_icm + - glimmer_extract + - glimmer_gbk_to_orf + - glimmer_glimmer_to_gff + - glimmer_long_orfs + - glimmer_knowledge_based + - glimmer_not_knowledge_based + Galaxy wrapper id: glimmer + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 4343 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4343 + No. of tool users (all time) (usegalaxy.eu): 4343 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4343 + Source: https://ccb.jhu.edu/software/glimmer/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 407 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 407 + Tool usage (all time) (usegalaxy.eu): 407 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 407 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 4 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 4 + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + biii: null + bio.tool description: GEMINI (GEnome MINIng) is a flexible framework for exploring + genetic variation in the context of the wealth of genome annotations available + for the human genome. By placing genetic variants, sample phenotypes and genotypes, + as well as genome annotations into an integrated database framework, GEMINI provides + a simple, flexible, and powerful system for exploring genetic variation for disease + and population genetics. + bio.tool id: gemini + bio.tool ids: + - gemini + bio.tool name: GEMINI +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: goenrichment + Conda version: 2.0.1 + Date of first commit of the suite: '2018-12-28' + Description: Performs GO Enrichment analysis. + EDAM operation: + - Gene-set enrichment analysis + EDAM operation (no superclasses): + - Gene-set enrichment analysis + EDAM topic: + - Transcriptomics + EDAM topic (no superclasses): + - Transcriptomics + Galaxy tool ids: + - goenrichment + - goslimmer + Galaxy wrapper id: goenrichment + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment + Galaxy wrapper version: 2.0.1 + No. of tool users (5 years) (usegalaxy.eu): 5800 + No. of tool users (5 years) (usegalaxy.org): 7756 + No. of tool users (5 years) (usegalaxy.org.au): 1149 + No. of tool users (5 years) - all main servers: 14705 + No. of tool users (all time) (usegalaxy.eu): 6212 + No. of tool users (all time) (usegalaxy.org): 7756 + No. of tool users (all time) (usegalaxy.org.au): 1149 + No. of tool users (all time) - all main servers: 15117 + Source: https://github.com/DanFaria/GOEnrichment + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 826 + Tool usage (5 years) (usegalaxy.org): 1048 + Tool usage (5 years) (usegalaxy.org.au): 215 + Tool usage (5 years) - all main servers: 2089 + Tool usage (all time) (usegalaxy.eu): 871 + Tool usage (all time) (usegalaxy.org): 1048 + Tool usage (all time) (usegalaxy.org.au): 215 + Tool usage (all time) - all main servers: 2134 + ToolShed categories: + - Genome annotation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: "GOEnrichment is a tool for performing GO enrichment analysis\ + \ of gene sets, such as those obtained from RNA-seq or Microarray experiments,\ + \ to help characterize them at the functional level. It is available in Galaxy\ + \ Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows\ + \ the user to use any version of the Gene Ontology and any GO annotation file\ + \ they desire. To enable the use of GO slims, it is accompanied by a sister tool\ + \ GOSlimmer, which can convert annotation files from full GO to any specified\ + \ GO slim.The tool features an optional graph clustering algorithm to reduce the\ + \ redundancy in the set of enriched GO terms and simplify its output.It was developed\ + \ by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ci\xEAncia." + bio.tool id: goenrichment + bio.tool ids: + - goenrichment + bio.tool name: GOEnrichment +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-goseq + Conda version: 1.54.0 + Date of first commit of the suite: '2018-09-30' + Description: goseq does selection-unbiased testing for category enrichment amongst + differentially expressed (DE) genes for RNA-seq data + EDAM operation: + - Gene functional annotation + EDAM operation (no superclasses): + - Gene functional annotation + EDAM topic: + - RNA-Seq + EDAM topic (no superclasses): + - RNA-Seq + Galaxy tool ids: + - goseq + Galaxy wrapper id: goseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq + Galaxy wrapper version: 1.50.0 + No. of tool users (5 years) (usegalaxy.eu): 20207 + No. of tool users (5 years) (usegalaxy.org): 24488 + No. of tool users (5 years) (usegalaxy.org.au): 4155 + No. of tool users (5 years) - all main servers: 48850 + No. of tool users (all time) (usegalaxy.eu): 21960 + No. of tool users (all time) (usegalaxy.org): 26198 + No. of tool users (all time) (usegalaxy.org.au): 4155 + No. of tool users (all time) - all main servers: 52313 + Source: https://bioconductor.org/packages/release/bioc/html/goseq.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2807 + Tool usage (5 years) (usegalaxy.org): 3066 + Tool usage (5 years) (usegalaxy.org.au): 545 + Tool usage (5 years) - all main servers: 6418 + Tool usage (all time) (usegalaxy.eu): 3139 + Tool usage (all time) (usegalaxy.org): 3321 + Tool usage (all time) (usegalaxy.org.au): 545 + Tool usage (all time) - all main servers: 7005 + ToolShed categories: + - Statistics + - RNA + - Micro-array Analysis + ToolShed id: goseq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Detect Gene Ontology and/or other user defined categories + which are over/under represented in RNA-seq data. + bio.tool id: goseq + bio.tool ids: + - goseq + bio.tool name: GOseq +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 0 + Conda id: r-gprofiler2 + Conda version: null + Date of first commit of the suite: '2019-10-30' + Description: functional enrichment analysis of gene lists, convertion between various + types of namespaces, translation gene identifiers between organisms and more + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gprofiler_convert + - gprofiler_gost + - gprofiler_orth + - gprofiler_random + - gprofiler_snpense + Galaxy wrapper id: gprofiler + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ + Galaxy wrapper version: '@TOOL_VERSION@+galaxy11' + No. of tool users (5 years) (usegalaxy.eu): 4001 + No. of tool users (5 years) (usegalaxy.org): 7882 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 11883 + No. of tool users (all time) (usegalaxy.eu): 4001 + No. of tool users (all time) (usegalaxy.org): 7882 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 11883 + Source: https://biit.cs.ut.ee/gprofiler + Status: To update + Tool usage (5 years) (usegalaxy.eu): 614 + Tool usage (5 years) (usegalaxy.org): 1238 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1852 + Tool usage (all time) (usegalaxy.eu): 614 + Tool usage (all time) (usegalaxy.org): 1238 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1852 + ToolShed categories: + - Statistics + - Web Services + ToolShed id: gprofiler + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: graph_embed + Conda version: '2.4' + Date of first commit of the suite: '2019-12-10' + Description: Compute a 2D embedding of a data matrix given supervised class information + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - graphembed + Galaxy wrapper id: graphembed + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ + Galaxy wrapper version: '2.4' + No. of tool users (5 years) (usegalaxy.eu): 78 + No. of tool users (5 years) (usegalaxy.org): 120 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 198 + No. of tool users (all time) (usegalaxy.eu): 78 + No. of tool users (all time) (usegalaxy.org): 120 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 198 + Source: https://github.com/fabriziocosta/GraphEmbed + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 43 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 49 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 43 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 49 + ToolShed categories: + - Statistics + - Graphics + ToolShed id: graphembed + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: graphlan + Conda version: 1.1.3 + Date of first commit of the suite: '2017-03-03' + Description: GraPhlAn is a software tool for producing high-quality circular representations + of taxonomic and phylogenetic trees + EDAM operation: + - Phylogenetic inference + - Phylogenetic tree visualisation + - Phylogenetic tree editing + - Taxonomic classification + EDAM operation (no superclasses): + - Phylogenetic inference + - Phylogenetic tree visualisation + - Phylogenetic tree editing + - Taxonomic classification + EDAM topic: + - Metagenomics + - Phylogenetics + - Phylogenomics + - Cladistics + EDAM topic (no superclasses): + - Metagenomics + - Phylogenetics + - Phylogenomics + - Cladistics + Galaxy tool ids: + - graphlan + - graphlan_annotate + Galaxy wrapper id: graphlan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 9816 + No. of tool users (5 years) (usegalaxy.org): 1273 + No. of tool users (5 years) (usegalaxy.org.au): 1104 + No. of tool users (5 years) - all main servers: 12193 + No. of tool users (all time) (usegalaxy.eu): 10927 + No. of tool users (all time) (usegalaxy.org): 1273 + No. of tool users (all time) (usegalaxy.org.au): 1104 + No. of tool users (all time) - all main servers: 13304 + Source: https://github.com/biobakery/graphlan + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1285 + Tool usage (5 years) (usegalaxy.org): 368 + Tool usage (5 years) (usegalaxy.org.au): 242 + Tool usage (5 years) - all main servers: 1895 + Tool usage (all time) (usegalaxy.eu): 1350 + Tool usage (all time) (usegalaxy.org): 368 + Tool usage (all time) (usegalaxy.org.au): 242 + Tool usage (all time) - all main servers: 1960 + ToolShed categories: + - Metagenomics + - Graphics + - Phylogenetics + ToolShed id: graphlan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: GraPhlAn is a software tool for producing high-quality circular + representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, + integrative, informative, and publication-ready representations of phylogenetically- + and taxonomically-driven investigation. + bio.tool id: graphlan + bio.tool ids: + - graphlan + bio.tool name: GraPhlAn +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: groot + Conda version: 1.1.2 + Date of first commit of the suite: '2024-05-14' + Description: GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic + samples + EDAM operation: + - Antimicrobial resistance prediction + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + EDAM topic: + - Metagenomics + - Microbiology + - Genomics + EDAM topic (no superclasses): + - Metagenomics + - Microbiology + Galaxy tool ids: + - groot + Galaxy wrapper id: groot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot + Galaxy wrapper version: 1.1.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/will-rowe/groot + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: groot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: Indexed variation graphs for efficient and accurate resistome + profiling. + bio.tool id: groot + bio.tool ids: + - groot + bio.tool name: GROOT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: gtdb_to_taxdump + Conda version: 0.1.9 + Date of first commit of the suite: '2024-08-25' + Description: Convert GTDB taxonomy to NCBI taxdump format + EDAM operation: + - Data handling + - Mapping + - Generation + EDAM operation (no superclasses): + - Data handling + - Mapping + - Generation + EDAM topic: + - Computational biology + EDAM topic (no superclasses): + - Computational biology + Galaxy tool ids: + - gtdb_to_taxdump + Galaxy wrapper id: gtdb_to_taxdump + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump + Galaxy wrapper source: https://github.com/nick-youngblut/gtdb_to_taxdump + Galaxy wrapper version: 0.1.9 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/nick-youngblut/gtdb_to_taxdump + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: gtdb_to_taxdump + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Tool with multiple functions. Main functions are to create + a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format + out of this data. This tool can also create a mapping between the taxonomy classification + between GTDB and NCBI. + bio.tool id: gtdb_to_taxdump + bio.tool ids: + - gtdb_to_taxdump + bio.tool name: gtdb_to_taxdump +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: gtdbtk + Conda version: 2.4.0 + Date of first commit of the suite: '2022-12-13' + Description: 'GTDB-Tk is a software tool kit for assigning objective taxonomic classifications + to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It + is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled + genomes (MAGs) to be obtained directly from environmental samples. It can alsobe + applied to isolate and single-cell genomes. ' + EDAM operation: + - Genome alignment + - Taxonomic classification + - Sequence assembly + - Query and retrieval + EDAM operation (no superclasses): + - Genome alignment + - Taxonomic classification + - Sequence assembly + - Query and retrieval + EDAM topic: + - Metagenomics + - Taxonomy + - Phylogenetics + - Database management + - Proteins + EDAM topic (no superclasses): + - Metagenomics + - Taxonomy + - Phylogenetics + - Database management + - Proteins + Galaxy tool ids: + - gtdbtk_classify_wf + Galaxy wrapper id: gtdbtk + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk + Galaxy wrapper version: 2.4.0 + No. of tool users (5 years) (usegalaxy.eu): 476 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 588 + No. of tool users (5 years) - all main servers: 1064 + No. of tool users (all time) (usegalaxy.eu): 476 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 588 + No. of tool users (all time) - all main servers: 1064 + Source: https://github.com/Ecogenomics/GTDBTk + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 87 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 74 + Tool usage (5 years) - all main servers: 161 + Tool usage (all time) (usegalaxy.eu): 87 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 74 + Tool usage (all time) - all main servers: 161 + ToolShed categories: + - Metagenomics + ToolShed id: gtdbtk + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: + a toolkit for assigning objective taxonomic classifications to bacterial and archaeal + genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications + to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. + It is designed to work with recent advances that allow hundreds or thousands of + metagenome-assembled genomes (MAGs) to be obtained directly from environmental + samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk + is open source and released under the GNU General Public License (Version 3).' + bio.tool id: GTDB-Tk + bio.tool ids: + - GTDB-Tk + bio.tool name: GTDB-Tk +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: ucsc-gtftogenepred + Conda version: '469' + Date of first commit of the suite: '2018-05-17' + Description: Convert GTF files to BED12 format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - gtftobed12 + Galaxy wrapper id: gtfToBed12 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 + Galaxy wrapper version: '357' + No. of tool users (5 years) (usegalaxy.eu): 8329 + No. of tool users (5 years) (usegalaxy.org): 8009 + No. of tool users (5 years) (usegalaxy.org.au): 1577 + No. of tool users (5 years) - all main servers: 17915 + No. of tool users (all time) (usegalaxy.eu): 9363 + No. of tool users (all time) (usegalaxy.org): 8009 + No. of tool users (all time) (usegalaxy.org.au): 1577 + No. of tool users (all time) - all main servers: 18949 + Source: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3336 + Tool usage (5 years) (usegalaxy.org): 3130 + Tool usage (5 years) (usegalaxy.org.au): 344 + Tool usage (5 years) - all main servers: 6810 + Tool usage (all time) (usegalaxy.eu): 3828 + Tool usage (all time) (usegalaxy.org): 3130 + Tool usage (all time) (usegalaxy.org.au): 344 + Tool usage (all time) - all main servers: 7302 + ToolShed categories: + - Convert Formats + ToolShed id: gtftobed12 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Utilities for handling sequences and assemblies from the UCSC + Genome Browser project. + bio.tool id: UCSC_Genome_Browser_Utilities + bio.tool ids: + - UCSC_Genome_Browser_Utilities + bio.tool name: UCSC Genome Browser Utilities +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: gubbins + Conda version: 3.3.5 + Date of first commit of the suite: '2017-06-22' + Description: Gubbins - bacterial recombination detection + EDAM operation: + - Genotyping + - Phylogenetic inference + - Ancestral reconstruction + EDAM operation (no superclasses): + - Genotyping + - Phylogenetic inference + - Ancestral reconstruction + EDAM topic: + - Phylogeny + - Genotype and phenotype + - Whole genome sequencing + EDAM topic (no superclasses): + - Phylogeny + - Genotype and phenotype + - Whole genome sequencing + Galaxy tool ids: + - gubbins + Galaxy wrapper id: gubbins + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins + Galaxy wrapper version: 3.2.1 + No. of tool users (5 years) (usegalaxy.eu): 3690 + No. of tool users (5 years) (usegalaxy.org): 3323 + No. of tool users (5 years) (usegalaxy.org.au): 1895 + No. of tool users (5 years) - all main servers: 8908 + No. of tool users (all time) (usegalaxy.eu): 3811 + No. of tool users (all time) (usegalaxy.org): 3323 + No. of tool users (all time) (usegalaxy.org.au): 2429 + No. of tool users (all time) - all main servers: 9563 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 326 + Tool usage (5 years) (usegalaxy.org): 235 + Tool usage (5 years) (usegalaxy.org.au): 234 + Tool usage (5 years) - all main servers: 795 + Tool usage (all time) (usegalaxy.eu): 336 + Tool usage (all time) (usegalaxy.org): 235 + Tool usage (all time) (usegalaxy.org.au): 258 + Tool usage (all time) - all main servers: 829 + ToolShed categories: + - Sequence Analysis + ToolShed id: gubbins + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Gubbins is a tool for rapid phylogenetic analysis of large + samples of recombinant bacterial whole genome sequences. + bio.tool id: gubbins + bio.tool ids: + - gubbins + bio.tool name: Gubbins +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: gvcftools + Conda version: 0.17.0 + Date of first commit of the suite: '2016-12-29' + Description: gvcftools is a set of utilities to help create and analyze Genome VCF + (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing + all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gvcftools_extract_variants + Galaxy wrapper id: gvcftools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/sequencing/gvcftools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-gwastools + Conda version: 1.48.0 + Date of first commit of the suite: '2019-10-07' + Description: null + EDAM operation: + - Deposition + - Analysis + - Annotation + EDAM operation (no superclasses): + - Deposition + - Analysis + - Annotation + EDAM topic: + - GWAS study + EDAM topic (no superclasses): + - GWAS study + Galaxy tool ids: + - gwastools_manhattan_plot + Galaxy wrapper id: gwastools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools + Galaxy wrapper source: null + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://bioconductor.org/packages/release/bioc/html/GWASTools.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Visualization + - Variant Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 1 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Classes for storing very large GWAS data sets and annotation, + and functions for GWAS data cleaning and analysis. + bio.tool id: gwastools + bio.tool ids: + - gwastools + bio.tool name: GWASTools +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hamronization + Conda version: 1.1.4 + Date of first commit of the suite: '2021-02-02' + Description: Convert AMR gene detection tool output to hAMRonization specification + format. + EDAM operation: + - Data handling + - Antimicrobial resistance prediction + - Parsing + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + - Parsing + EDAM topic: + - Public health and epidemiology + - Microbiology + - Bioinformatics + EDAM topic (no superclasses): + - Public health and epidemiology + - Microbiology + - Bioinformatics + Galaxy tool ids: + - hamronize_summarize + - hamronize_tool + Galaxy wrapper id: hamronization + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization + Galaxy wrapper version: 1.1.4 + No. of tool users (5 years) (usegalaxy.eu): 7303 + No. of tool users (5 years) (usegalaxy.org): 20 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7323 + No. of tool users (all time) (usegalaxy.eu): 7303 + No. of tool users (all time) (usegalaxy.org): 20 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7323 + Source: https://github.com/pha4ge/hAMRonization + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 222 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 224 + Tool usage (all time) (usegalaxy.eu): 222 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 224 + ToolShed categories: + - Sequence Analysis + ToolShed id: hamronization + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + biii: null + bio.tool description: Parse multiple Antimicrobial Resistance Analysis Reports into + a common data structure + bio.tool id: hamronization + bio.tool ids: + - hamronization + bio.tool name: hAMRonization +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bio_hansel + Conda version: 2.6.1 + Date of first commit of the suite: '2017-09-29' + Description: Heidelberg and Enteritidis SNP Elucidation + EDAM operation: + - Genotyping + - SNP detection + - Genome assembly + EDAM operation (no superclasses): + - Genotyping + - SNP detection + - Genome assembly + EDAM topic: + - Whole genome sequencing + - DNA polymorphism + - Genotype and phenotype + - Infectious disease + - Agricultural science + EDAM topic (no superclasses): + - Whole genome sequencing + - DNA polymorphism + - Genotype and phenotype + - Infectious disease + - Agricultural science + Galaxy tool ids: + - bio_hansel + Galaxy wrapper id: hansel + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel + Galaxy wrapper version: 2.6.1 + No. of tool users (5 years) (usegalaxy.eu): 349 + No. of tool users (5 years) (usegalaxy.org): 364 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 713 + No. of tool users (all time) (usegalaxy.eu): 359 + No. of tool users (all time) (usegalaxy.org): 364 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 723 + Source: https://github.com/phac-nml/bio_hansel + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 53 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 85 + Tool usage (all time) (usegalaxy.eu): 33 + Tool usage (all time) (usegalaxy.org): 53 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 86 + ToolShed categories: + - Sequence Analysis + ToolShed id: bio_hansel + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: BioHansel is a tool for performing high-resolution genotyping + of bacterial isolates by identifying phylogenetically informative single nucleotide + polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing + (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen + WGS data to canonical SNPs contained in hierarchically structured schemas and + assigns genotypes based on the detected SNP profile. + bio.tool id: Biohansel + bio.tool ids: + - Biohansel + bio.tool name: BioHansel +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: hapcut2 + Conda version: 1.3.4 + Date of first commit of the suite: '2022-10-19' + Description: Robust and accurate haplotype assembly for diverse sequencing technologies + EDAM operation: + - Haplotype mapping + - Variant classification + EDAM operation (no superclasses): + - Haplotype mapping + - Variant classification + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hapcut2 + Galaxy wrapper id: hapcut2 + Galaxy wrapper owner: galaxy-australia + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc + Galaxy wrapper version: 1.3.4 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 103 + No. of tool users (5 years) - all main servers: 103 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 103 + No. of tool users (all time) - all main servers: 103 + Source: https://github.com/vibansal/HapCUT2 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Assembly + ToolShed id: hapcut2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: 'HapCUT2 is a maximum-likelihood-based tool for assembling + haplotypes from DNA sequence reads, designed to "just work" with excellent speed + and accuracy across a range of long- and short-read sequencing technologies.The + output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md' + bio.tool id: hapcut2 + bio.tool ids: + - hapcut2 + bio.tool name: HapCUT2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hapog + Conda version: 1.3.8 + Date of first commit of the suite: '2022-09-16' + Description: Hapo-G - Haplotype-Aware Polishing of Genomes + EDAM operation: + - Genome assembly + - Optimisation and refinement + EDAM operation (no superclasses): + - Genome assembly + - Optimisation and refinement + EDAM topic: + - Sequence assembly + - Genomics + EDAM topic (no superclasses): + - Sequence assembly + - Genomics + Galaxy tool ids: + - hapog + Galaxy wrapper id: hapog + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog + Galaxy wrapper version: 1.3.8 + No. of tool users (5 years) (usegalaxy.eu): 502 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 502 + No. of tool users (all time) (usegalaxy.eu): 502 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 502 + Source: https://github.com/institut-de-genomique/HAPO-G + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 66 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 66 + Tool usage (all time) (usegalaxy.eu): 66 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 66 + ToolShed categories: + - Assembly + ToolShed id: hapog + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Hapo-G is a tool that aims to improve the quality of genome + assemblies by polishing the consensus with accurate reads. It capable of incorporating + phasing information from high-quality reads (short or long-reads) to polish genome + assemblies and in particular assemblies of diploid and heterozygous genomes. + bio.tool id: hapog + bio.tool ids: + - hapog + bio.tool name: Hapo-G +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hap.py + Conda version: 0.3.15 + Date of first commit of the suite: '2022-01-25' + Description: A tool to perform comparisons only based on chromosome, position, and + allele identity for comparison of somatic callsets. + EDAM operation: + - Variant calling + - Sequence analysis + - Genotyping + EDAM operation (no superclasses): + - Variant calling + - Sequence analysis + - Genotyping + EDAM topic: + - Genomics + - DNA polymorphism + EDAM topic (no superclasses): + - Genomics + - DNA polymorphism + Galaxy tool ids: + - som.py + Galaxy wrapper id: happy + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy + Galaxy wrapper version: 0.3.14 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/Illumina/hap.py + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: happy + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: This is a set of programs based on htslib to benchmark variant + calls against gold standard truth datasets.To compare a VCF against a gold standard + dataset, use the following commmand line to perform genotype-level haplotype comparison. + bio.tool id: hap.py + bio.tool ids: + - hap.py + bio.tool name: hap.py +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-gplots + Conda version: 2.17.0 + Date of first commit of the suite: '2019-02-10' + Description: heatmap.2 function from the R gplots package + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ggplot2_heatmap2 + Galaxy wrapper id: heatmap2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 + Galaxy wrapper version: 3.2.0 + No. of tool users (5 years) (usegalaxy.eu): 46700 + No. of tool users (5 years) (usegalaxy.org): 64214 + No. of tool users (5 years) (usegalaxy.org.au): 7783 + No. of tool users (5 years) - all main servers: 118697 + No. of tool users (all time) (usegalaxy.eu): 50808 + No. of tool users (all time) (usegalaxy.org): 70429 + No. of tool users (all time) (usegalaxy.org.au): 7912 + No. of tool users (all time) - all main servers: 129149 + Source: https://github.com/cran/gplots + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4645 + Tool usage (5 years) (usegalaxy.org): 5799 + Tool usage (5 years) (usegalaxy.org.au): 704 + Tool usage (5 years) - all main servers: 11148 + Tool usage (all time) (usegalaxy.eu): 5114 + Tool usage (all time) (usegalaxy.org): 6830 + Tool usage (all time) (usegalaxy.org.au): 724 + Tool usage (all time) - all main servers: 12668 + ToolShed categories: + - Visualization + ToolShed id: ggplot2_heatmap2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 4 + Conda id: bioconductor-bionet + Conda version: 1.62.0 + Date of first commit of the suite: '2018-06-11' + Description: An algorithm for identification of the optimal scoring subnetwork. + EDAM operation: + - Pathway or network analysis + EDAM operation (no superclasses): + - Pathway or network analysis + EDAM topic: + - Genetics + - Gene expression + - Molecular interactions, pathways and networks + EDAM topic (no superclasses): + - Genetics + - Gene expression + - Molecular interactions, pathways and networks + Galaxy tool ids: + - heinz_bum + - heinz + - heinz_scoring + - heinz_visualization + Galaxy wrapper id: heinz + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 1281 + No. of tool users (5 years) (usegalaxy.org): 1559 + No. of tool users (5 years) (usegalaxy.org.au): 678 + No. of tool users (5 years) - all main servers: 3518 + No. of tool users (all time) (usegalaxy.eu): 1434 + No. of tool users (all time) (usegalaxy.org): 1559 + No. of tool users (all time) (usegalaxy.org.au): 678 + No. of tool users (all time) - all main servers: 3671 + Source: https://github.com/ls-cwi/heinz + Status: To update + Tool usage (5 years) (usegalaxy.eu): 367 + Tool usage (5 years) (usegalaxy.org): 636 + Tool usage (5 years) (usegalaxy.org.au): 52 + Tool usage (5 years) - all main servers: 1055 + Tool usage (all time) (usegalaxy.eu): 442 + Tool usage (all time) (usegalaxy.org): 636 + Tool usage (all time) (usegalaxy.org.au): 52 + Tool usage (all time) - all main servers: 1130 + ToolShed categories: + - Transcriptomics + - Visualization + - Statistics + ToolShed id: heinz + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 4 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 4 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 4 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 4 + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.no: 4 + UseGalaxy.or: 4 + biii: null + bio.tool description: Tool for single-species active module discovery. + bio.tool id: heinz + bio.tool ids: + - heinz + - bionet + bio.tool name: Heinz +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-06-07' + Description: Parsing and building variant descriptor strings compliant with the + HGVS standard + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hgvsparser + Galaxy wrapper id: hgvsparser + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 6346 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6346 + No. of tool users (all time) (usegalaxy.eu): 6346 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6346 + Source: https://github.com/VariantEffect/hgvsParseR/tree/master + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Variant Analysis + ToolShed id: hgvsparser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 38 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 38 + Available on UseGalaxy.org.au: 38 + Conda id: hicexplorer + Conda version: 3.7.5 + Date of first commit of the suite: '2020-03-12' + Description: 'HiCExplorer: Set of programs to process, analyze and visualize Hi-C + data.' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hicexplorer_chicaggregatestatistic + - hicexplorer_chicdifferentialtest + - hicexplorer_chicexportdata + - hicexplorer_chicplotviewpoint + - hicexplorer_chicqualitycontrol + - hicexplorer_chicsignificantinteractions + - hicexplorer_chicviewpoint + - hicexplorer_chicviewpointbackgroundmodel + - hicexplorer_hicadjustmatrix + - hicexplorer_hicaggregatecontacts + - hicexplorer_hicaverageregions + - hicexplorer_hicbuildmatrix + - hicexplorer_hiccomparematrices + - hicexplorer_hiccompartmentspolarization + - hicexplorer_hicconvertformat + - hicexplorer_hiccorrectmatrix + - hicexplorer_hiccorrelate + - hicexplorer_hicdetectloops + - hicexplorer_hicdifferentialtad + - hicexplorer_hicfindrestrictionsites + - hicexplorer_hicfindtads + - hicexplorer_hichyperoptDetectLoops + - hicexplorer_hicinfo + - hicexplorer_hicinterintratad + - hicexplorer_hicmergedomains + - hicexplorer_hicmergeloops + - hicexplorer_hicmergematrixbins + - hicexplorer_hicnormalize + - hicexplorer_hicpca + - hicexplorer_hicplotaverageregions + - hicexplorer_hicplotdistvscounts + - hicexplorer_hicplotmatrix + - hicexplorer_hicplotsvl + - hicexplorer_hicplotviewpoint + - hicexplorer_hicquickqc + - hicexplorer_hicsummatrices + - hicexplorer_hictransform + - hicexplorer_hicvalidatelocations + Galaxy wrapper id: hicexplorer + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer + Galaxy wrapper version: 3.7.5 + No. of tool users (5 years) (usegalaxy.eu): 44449 + No. of tool users (5 years) (usegalaxy.org): 46 + No. of tool users (5 years) (usegalaxy.org.au): 1328 + No. of tool users (5 years) - all main servers: 45823 + No. of tool users (all time) (usegalaxy.eu): 68602 + No. of tool users (all time) (usegalaxy.org): 46 + No. of tool users (all time) (usegalaxy.org.au): 1328 + No. of tool users (all time) - all main servers: 69976 + Source: https://github.com/deeptools/HiCExplorer + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 3236 + Tool usage (5 years) (usegalaxy.org): 21 + Tool usage (5 years) (usegalaxy.org.au): 67 + Tool usage (5 years) - all main servers: 3324 + Tool usage (all time) (usegalaxy.eu): 4177 + Tool usage (all time) (usegalaxy.org): 21 + Tool usage (all time) (usegalaxy.org.au): 67 + Tool usage (all time) - all main servers: 4265 + ToolShed categories: + - Sequence Analysis + - Visualization + ToolShed id: hicexplorer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 13 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 33 + Tools available on UseGalaxy.cz: 36 + Tools available on UseGalaxy.eu: 38 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 33 + Tools available on UseGalaxy.org (Main): 38 + Tools available on UseGalaxy.org.au: 38 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 33 + UseGalaxy.cz: 36 + UseGalaxy.eu: 38 + UseGalaxy.fr: 13 + UseGalaxy.no: 33 + UseGalaxy.or: 38 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hicstuff + Conda version: 3.2.3 + Date of first commit of the suite: '2022-11-25' + Description: A toolkit to generate and manipulate Hi-C matrices + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hicstuff_pipeline + Galaxy wrapper id: hicstuff + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff + Galaxy wrapper version: 3.2.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/koszullab/hicstuff + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: hifiasm + Conda version: 0.20.0 + Date of first commit of the suite: '2024-07-11' + Description: A fast haplotype-resolved de novo assembler + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hifiasm + Galaxy wrapper id: hifiasm + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm + Galaxy wrapper source: https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm + Galaxy wrapper version: 0.19.9 + No. of tool users (5 years) (usegalaxy.eu): 1819 + No. of tool users (5 years) (usegalaxy.org): 1334 + No. of tool users (5 years) (usegalaxy.org.au): 2472 + No. of tool users (5 years) - all main servers: 5625 + No. of tool users (all time) (usegalaxy.eu): 1819 + No. of tool users (all time) (usegalaxy.org): 1334 + No. of tool users (all time) (usegalaxy.org.au): 2472 + No. of tool users (all time) - all main servers: 5625 + Source: https://github.com/chhylp123/hifiasm + Status: To update + Tool usage (5 years) (usegalaxy.eu): 539 + Tool usage (5 years) (usegalaxy.org): 389 + Tool usage (5 years) (usegalaxy.org.au): 137 + Tool usage (5 years) - all main servers: 1065 + Tool usage (all time) (usegalaxy.eu): 539 + Tool usage (all time) (usegalaxy.org): 389 + Tool usage (all time) (usegalaxy.org.au): 137 + Tool usage (all time) - all main servers: 1065 + ToolShed categories: + - Assembly + ToolShed id: hifiasm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: hifiasm_meta + Conda version: hamtv0.3.1 + Date of first commit of the suite: '2023-01-18' + Description: A hifiasm fork for metagenome assembly using Hifi reads. + EDAM operation: + - Sequence assembly + EDAM operation (no superclasses): + - Sequence assembly + EDAM topic: + - Sequence assembly + - Metagenomics + EDAM topic (no superclasses): + - Sequence assembly + - Metagenomics + Galaxy tool ids: + - hifiasm_meta + Galaxy wrapper id: hifiasm_meta + Galaxy wrapper owner: galaxy-australia + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta + Galaxy wrapper version: 0.3.1 + No. of tool users (5 years) (usegalaxy.eu): 156 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 220 + No. of tool users (5 years) - all main servers: 376 + No. of tool users (all time) (usegalaxy.eu): 156 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 220 + No. of tool users (all time) - all main servers: 376 + Source: https://github.com/xfengnefx/hifiasm-meta + Status: To update + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 11 + Tool usage (5 years) - all main servers: 31 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 11 + Tool usage (all time) - all main servers: 31 + ToolShed categories: + - Metagenomics + ToolShed id: hifiasm_meta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Hifiasm_meta - de novo metagenome assembler, based on hifiasm, + a haplotype-resolved de novo assembler for PacBio Hifi reads. + bio.tool id: hifiasm-meta + bio.tool ids: + - hifiasm-meta + bio.tool name: Hifiasm-meta +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: hisat2 + Conda version: 2.2.1 + Date of first commit of the suite: '2020-11-24' + Description: HISAT2 is a fast and sensitive spliced alignment program. + EDAM operation: + - Sequence alignment + EDAM operation (no superclasses): + - Sequence alignment + EDAM topic: + - RNA-seq + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hisat2 + Galaxy wrapper id: hisat2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 337151 + No. of tool users (5 years) (usegalaxy.org): 699868 + No. of tool users (5 years) (usegalaxy.org.au): 87016 + No. of tool users (5 years) - all main servers: 1124035 + No. of tool users (all time) (usegalaxy.eu): 353499 + No. of tool users (all time) (usegalaxy.org): 896164 + No. of tool users (all time) (usegalaxy.org.au): 94859 + No. of tool users (all time) - all main servers: 1344522 + Source: http://ccb.jhu.edu/software/hisat2/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 10046 + Tool usage (5 years) (usegalaxy.org): 26656 + Tool usage (5 years) (usegalaxy.org.au): 5302 + Tool usage (5 years) - all main servers: 42004 + Tool usage (all time) (usegalaxy.eu): 10719 + Tool usage (all time) (usegalaxy.org): 34018 + Tool usage (all time) (usegalaxy.org.au): 5695 + Tool usage (all time) - all main servers: 50432 + ToolShed categories: + - Assembly + ToolShed id: hisat2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Alignment program for mapping next-generation sequencing reads + (both DNA and RNA) to a population of human genomes (as well as to a single reference + genome). + bio.tool id: hisat2 + bio.tool ids: + - hisat2 + bio.tool name: HISAT2 +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python-hivclustering + Conda version: 1.8.0 + Date of first commit of the suite: '2018-06-06' + Description: Infers transmission networks from pairwise distances inferred by tn93 + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hivclustering + Galaxy wrapper id: hivclustering + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ + Galaxy wrapper version: 1.3.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://pypi.org/project/hivclustering/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Next Gen Mappers + ToolShed id: hivclustering + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 12 + Available on UseGalaxy.fr: 12 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 12 + Conda id: hmmer + Conda version: '3.4' + Date of first commit of the suite: '2016-11-14' + Description: HMMER is used for searching sequence databases for homologs of proteinsequences, + and for making protein sequence alignments. It implementsmethods using probabilistic + models called profile hidden Markov models(profile HMMs). + EDAM operation: + - Formatting + - Multiple sequence alignment + - Sequence profile generation + - Format validation + - Conversion + - Sequence generation + - Data retrieval + - Statistical calculation + - Database search + - Formatting + - Database search + - Database search + - Probabilistic sequence generation + - Statistical calculation + - Statistical calculation + - Sequence database search + - Formatting + - Sequence database search + - Database search + - Sequence database search + EDAM operation (no superclasses): + - Formatting + - Multiple sequence alignment + - Sequence profile generation + - Format validation + - Conversion + - Data retrieval + - Statistical calculation + - Formatting + - Probabilistic sequence generation + - Statistical calculation + - Statistical calculation + - Sequence database search + - Formatting + - Sequence database search + - Sequence database search + EDAM topic: + - Sequence analysis + - Sequence sites, features and motifs + - Gene and protein families + EDAM topic (no superclasses): + - Sequence analysis + - Sequence sites, features and motifs + - Gene and protein families + Galaxy tool ids: + - hmmer_alimask + - hmmer_hmmalign + - hmmer_hmmbuild + - hmmer_hmmconvert + - hmmer_hmmemit + - hmmer_hmmfetch + - hmmer_hmmscan + - hmmer_hmmsearch + - hmmer_jackhmmer + - hmmer_nhmmer + - hmmer_nhmmscan + - hmmer_phmmer + Galaxy wrapper id: hmmer3 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 + Galaxy wrapper version: '3.4' + No. of tool users (5 years) (usegalaxy.eu): 35919 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 3023 + No. of tool users (5 years) - all main servers: 38942 + No. of tool users (all time) (usegalaxy.eu): 36952 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 3023 + No. of tool users (all time) - all main servers: 39975 + Source: http://hmmer.org/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1283 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 180 + Tool usage (5 years) - all main servers: 1463 + Tool usage (all time) (usegalaxy.eu): 1321 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 180 + Tool usage (all time) - all main servers: 1501 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 12 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 12 + Tools available on UseGalaxy.cz: 12 + Tools available on UseGalaxy.eu: 12 + Tools available on UseGalaxy.fr: 12 + Tools available on UseGalaxy.no: 12 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 12 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 12 + UseGalaxy.cz: 12 + UseGalaxy.eu: 12 + UseGalaxy.fr: 12 + UseGalaxy.no: 12 + UseGalaxy.or: 12 + biii: null + bio.tool description: This tool is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It implements + methods using probabilistic models called profile hidden Markov models. The new + HMMER3 project, HMMER is now as fast as BLAST for protein search. + bio.tool id: hmmer3 + bio.tool ids: + - hmmer3 + bio.tool name: HMMER3 +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: homer + Conda version: '4.11' + Date of first commit of the suite: '2021-08-08' + Description: HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite + of tools for Motif Discovery and next-gen sequencing analysis. + EDAM operation: + - Sequence motif discovery + EDAM operation (no superclasses): + - Sequence motif discovery + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - homer_annotatePeaks + - homer_findMotifs + - homer_findMotifsGenome + - homer_gtf_to_annotations + - homer_scanMotifGenomeWide + Galaxy wrapper id: homer + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer + Galaxy wrapper version: '4.11' + No. of tool users (5 years) (usegalaxy.eu): 8531 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 8531 + No. of tool users (all time) (usegalaxy.eu): 8531 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8531 + Source: http://homer.ucsd.edu/homer/index.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 633 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 633 + Tool usage (all time) (usegalaxy.eu): 633 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 633 + ToolShed categories: + - Sequence Analysis + ToolShed id: data_manager_homer_preparse + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 2 + biii: null + bio.tool description: HOMER contains a novel motif discovery algorithm that was + designed for regulatory element analysis in genomics applications (DNA only, no + protein). It is a differential motif discovery algorithm, which means that it + takes two sets of sequences and tries to identify the regulatory elements that + are specifically enriched in on set relative to the other. It uses ZOOPS scoring + (zero or one occurrence per sequence) coupled with the hypergeometric enrichment + calculations (or binomial) to determine motif enrichment. HOMER also tries its + best to account for sequenced bias in the dataset. It was designed with ChIP-Seq + and promoter analysis in mind, but can be applied to pretty much any nucleic acids + motif finding problem. + bio.tool id: homer + bio.tool ids: + - homer + bio.tool name: homer +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: htseq + Conda version: 2.0.5 + Date of first commit of the suite: '2017-01-06' + Description: Count aligned reads (SAM/BAM) that overlap genomic features (GFF) + EDAM operation: + - Nucleic acid sequence analysis + EDAM operation (no superclasses): + - Nucleic acid sequence analysis + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - htseq_count + Galaxy wrapper id: htseq_count + Galaxy wrapper owner: lparsons + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count + Galaxy wrapper version: 2.0.5 + No. of tool users (5 years) (usegalaxy.eu): 144907 + No. of tool users (5 years) (usegalaxy.org): 213407 + No. of tool users (5 years) (usegalaxy.org.au): 27209 + No. of tool users (5 years) - all main servers: 385523 + No. of tool users (all time) (usegalaxy.eu): 168824 + No. of tool users (all time) (usegalaxy.org): 346792 + No. of tool users (all time) (usegalaxy.org.au): 33124 + No. of tool users (all time) - all main servers: 548740 + Source: https://readthedocs.org/projects/htseq/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 3703 + Tool usage (5 years) (usegalaxy.org): 10798 + Tool usage (5 years) (usegalaxy.org.au): 2613 + Tool usage (5 years) - all main servers: 17114 + Tool usage (all time) (usegalaxy.eu): 4366 + Tool usage (all time) (usegalaxy.org): 16485 + Tool usage (all time) (usegalaxy.org.au): 2854 + Tool usage (all time) - all main servers: 23705 + ToolShed categories: + - Genomic Interval Operations + - SAM + - Sequence Analysis + - RNA + ToolShed id: htseq_count + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Python framework to process and analyse high-throughput sequencing + (HTS) data + bio.tool id: htseq + bio.tool ids: + - htseq + bio.tool name: HTSeq +- Available on UseGalaxy.eu: 10 + Available on UseGalaxy.fr: 10 + Available on UseGalaxy.org (Main): 6 + Available on UseGalaxy.org.au: 10 + Conda id: humann + Conda version: '3.9' + Date of first commit of the suite: '2021-05-12' + Description: HUMAnN for functionally profiling metagenomes and metatranscriptomes + at species-level resolution + EDAM operation: + - Species frequency estimation + - Taxonomic classification + - Phylogenetic analysis + EDAM operation (no superclasses): + - Species frequency estimation + - Taxonomic classification + - Phylogenetic analysis + EDAM topic: + - Metagenomics + - Phylogenomics + EDAM topic (no superclasses): + - Metagenomics + - Phylogenomics + Galaxy tool ids: + - humann + - humann_barplot + - humann_join_tables + - humann_reduce_table + - humann_regroup_table + - humann_rename_table + - humann_renorm_table + - humann_split_stratified_table + - humann_split_table + - humann_unpack_pathways + Galaxy wrapper id: humann + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann + Galaxy wrapper version: '3.9' + No. of tool users (5 years) (usegalaxy.eu): 26659 + No. of tool users (5 years) (usegalaxy.org): 865 + No. of tool users (5 years) (usegalaxy.org.au): 3238 + No. of tool users (5 years) - all main servers: 30762 + No. of tool users (all time) (usegalaxy.eu): 26659 + No. of tool users (all time) (usegalaxy.org): 865 + No. of tool users (all time) (usegalaxy.org.au): 3238 + No. of tool users (all time) - all main servers: 30762 + Source: http://huttenhower.sph.harvard.edu/humann + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2067 + Tool usage (5 years) (usegalaxy.org): 174 + Tool usage (5 years) (usegalaxy.org.au): 351 + Tool usage (5 years) - all main servers: 2592 + Tool usage (all time) (usegalaxy.eu): 2067 + Tool usage (all time) (usegalaxy.org): 174 + Tool usage (all time) (usegalaxy.org.au): 351 + Tool usage (all time) - all main servers: 2592 + ToolShed categories: + - Metagenomics + ToolShed id: humann + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 10 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 10 + Tools available on UseGalaxy.eu: 10 + Tools available on UseGalaxy.fr: 10 + Tools available on UseGalaxy.no: 10 + Tools available on UseGalaxy.org (Main): 6 + Tools available on UseGalaxy.org.au: 10 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 10 + UseGalaxy.eu: 10 + UseGalaxy.fr: 10 + UseGalaxy.no: 10 + UseGalaxy.or: 10 + biii: null + bio.tool description: "HUMAnN is a pipeline for efficiently and accurately profiling\ + \ the presence/absence and abundance of microbial pathways in a community from\ + \ metagenomic or metatranscriptomic sequencing data (typically millions of short\ + \ DNA/RNA reads). This process, referred to as functional profiling, aims to describe\ + \ the metabolic potential of a microbial community and its members. More generally,\ + \ functional profiling answers the question \u201CWhat are the microbes in my\ + \ community-of-interest doing (or are capable of doing)?\u201D" + bio.tool id: humann + bio.tool ids: + - humann + bio.tool name: humann +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: hybpiper + Conda version: 2.3.0 + Date of first commit of the suite: '2023-09-04' + Description: Analyse targeted sequence capture data + EDAM operation: + - Sequence trimming + - Sequence assembly + - Read mapping + EDAM operation (no superclasses): + - Sequence trimming + - Sequence assembly + - Read mapping + EDAM topic: + - Phylogenetics + - Plant biology + - Gene transcripts + - Sequence assembly + - Phylogenomics + EDAM topic (no superclasses): + - Phylogenetics + - Plant biology + - Gene transcripts + - Sequence assembly + - Phylogenomics + Galaxy tool ids: + - hybpiper + Galaxy wrapper id: hybpiper + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper + Galaxy wrapper version: 2.1.6 + No. of tool users (5 years) (usegalaxy.eu): 1571 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 144 + No. of tool users (5 years) - all main servers: 1715 + No. of tool users (all time) (usegalaxy.eu): 1571 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 144 + No. of tool users (all time) - all main servers: 1715 + Source: https://github.com/mossmatters/HybPiper + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - Sequence Analysis + - Phylogenetics + ToolShed id: hybpiper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'Paralogs and off-target sequences improve phylogenetic resolution + in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering + genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- + Read our article in Applications in Plant Sciences (Open Access).HybPiper was + designed for targeted sequence capture, in which DNA sequencing libraries are + enriched for gene regions of interest, especially for phylogenetics. HybPiper + is a suite of Python scripts that wrap and connect bioinformatics tools in order + to extract target sequences from high-throughput DNA sequencing reads.' + bio.tool id: HybPiper + bio.tool ids: + - HybPiper + bio.tool name: HybPiper +- Available on UseGalaxy.eu: 17 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 17 + Available on UseGalaxy.org.au: 2 + Conda id: hyphy + Conda version: 2.5.62 + Date of first commit of the suite: '2021-04-19' + Description: Hypothesis Testing using Phylogenies + EDAM operation: + - Statistical calculation + EDAM operation (no superclasses): + - Statistical calculation + EDAM topic: + - Phylogeny + - Small molecules + - Molecular interactions, pathways and networks + EDAM topic (no superclasses): + - Phylogeny + - Small molecules + - Molecular interactions, pathways and networks + Galaxy tool ids: + - hyphy_absrel + - hyphy_annotate + - hyphy_bgm + - hyphy_busted + - hyphy_cfel + - hyphy_conv + - hyphy_fade + - hyphy_fel + - hyphy_fubar + - hyphy_gard + - hyphy_meme + - hyphy_prime + - hyphy_relax + - hyphy_slac + - hyphy_sm19 + - hyphy_strike_ambigs + - hyphy_summary + Galaxy wrapper id: hyphy + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ + Galaxy wrapper version: 2.5.47 + No. of tool users (5 years) (usegalaxy.eu): 11429 + No. of tool users (5 years) (usegalaxy.org): 7751 + No. of tool users (5 years) (usegalaxy.org.au): 715 + No. of tool users (5 years) - all main servers: 19895 + No. of tool users (all time) (usegalaxy.eu): 11429 + No. of tool users (all time) (usegalaxy.org): 7751 + No. of tool users (all time) (usegalaxy.org.au): 715 + No. of tool users (all time) - all main servers: 19895 + Source: http://www.hyphy.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 428 + Tool usage (5 years) (usegalaxy.org): 676 + Tool usage (5 years) (usegalaxy.org.au): 58 + Tool usage (5 years) - all main servers: 1162 + Tool usage (all time) (usegalaxy.eu): 428 + Tool usage (all time) (usegalaxy.org): 676 + Tool usage (all time) (usegalaxy.org.au): 58 + Tool usage (all time) - all main servers: 1162 + ToolShed categories: + - Phylogenetics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 12 + Tools available on UseGalaxy.cz: 17 + Tools available on UseGalaxy.eu: 17 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 12 + Tools available on UseGalaxy.org (Main): 17 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 12 + UseGalaxy.cz: 17 + UseGalaxy.eu: 17 + UseGalaxy.fr: 2 + UseGalaxy.no: 12 + UseGalaxy.or: 2 + biii: null + bio.tool description: Software package for the analysis of genetic sequences using + techniques in phylogenetics, molecular evolution, and machine learning. + bio.tool id: HyPhy + bio.tool ids: + - HyPhy + bio.tool name: HyPhy +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: hypo + Conda version: 1.0.3 + Date of first commit of the suite: '2021-11-15' + Description: Super Fast & Accurate Polisher for Long Read Genome Assemblies + EDAM operation: + - Optimisation and refinement + - Genome assembly + EDAM operation (no superclasses): + - Optimisation and refinement + - Genome assembly + EDAM topic: + - Sequence assembly + - Genomics + EDAM topic (no superclasses): + - Sequence assembly + - Genomics + Galaxy tool ids: + - hypo + Galaxy wrapper id: hypo + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo + Galaxy wrapper version: 1.0.3 + No. of tool users (5 years) (usegalaxy.eu): 473 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 473 + No. of tool users (all time) (usegalaxy.eu): 473 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 473 + Source: https://github.com/kensung-lab/hypo + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 93 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 93 + Tool usage (all time) (usegalaxy.eu): 93 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 93 + ToolShed categories: + - Assembly + ToolShed id: hypo + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: HyPo, a Hybrid Polisher, utilizes short as well as long reads + within a single run to polish a long reads assembly of small and large genomes. + bio.tool id: HyPo + bio.tool ids: + - HyPo + bio.tool name: HyPo +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: icescreen + Conda version: 1.3.2 + Date of first commit of the suite: '2022-01-04' + Description: ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative + Mobilizable Elements (IMEs) in Bacillota genomes. + EDAM operation: + - Database search + - Protein feature detection + EDAM operation (no superclasses): + - Database search + - Protein feature detection + EDAM topic: + - Mobile genetic elements + - Sequence sites, features and motifs + - Genomics + - Molecular interactions, pathways and networks + - Structural variation + EDAM topic (no superclasses): + - Mobile genetic elements + - Sequence sites, features and motifs + - Genomics + - Molecular interactions, pathways and networks + - Structural variation + Galaxy tool ids: + - icescreen + Galaxy wrapper id: icescreen + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen + Galaxy wrapper source: https://forgemia.inra.fr/ices_imes_analysis/icescreen + Galaxy wrapper version: 1.3.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://icescreen.migale.inrae.fr/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Genome annotation + ToolShed id: icescreen + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: A tool to detect Firmicute ICEs and IMEs, isolated or enclosed + in composite structures. + bio.tool id: icescreen + bio.tool ids: + - icescreen + bio.tool name: ICEscreen +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 0 + Conda id: idba + Conda version: 1.1.3 + Date of first commit of the suite: '2018-04-26' + Description: Wrappers for the idba assembler variants. + EDAM operation: + - Sequence assembly + EDAM operation (no superclasses): + - Sequence assembly + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - idba_hybrid + - idba_tran + - idba_ud + Galaxy wrapper id: idba_ud + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 1200 + No. of tool users (5 years) (usegalaxy.org): 1588 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2788 + No. of tool users (all time) (usegalaxy.eu): 1220 + No. of tool users (all time) (usegalaxy.org): 1588 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2808 + Source: https://i.cs.hku.hk/~alse/hkubrg/projects/index.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 187 + Tool usage (5 years) (usegalaxy.org): 267 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 454 + Tool usage (all time) (usegalaxy.eu): 195 + Tool usage (all time) (usegalaxy.org): 267 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 462 + ToolShed categories: + - Assembly + ToolShed id: idba + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: A short read assembler based on iterative De Bruijn graph. + It is developed under 64-bit Linux, but should be suitable for all unix-like system. + bio.tool id: idba + bio.tool ids: + - idba + bio.tool name: IDBA +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: idr + Conda version: 2.0.4.2 + Date of first commit of the suite: '2017-08-21' + Description: Galaxy wrappers for the IDR package from Nathan Boleu + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - idr + Galaxy wrapper id: idr + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ + Galaxy wrapper version: 2.0.3 + No. of tool users (5 years) (usegalaxy.eu): 2953 + No. of tool users (5 years) (usegalaxy.org): 1710 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4663 + No. of tool users (all time) (usegalaxy.eu): 3027 + No. of tool users (all time) (usegalaxy.org): 1710 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4737 + Source: https://github.com/nboley/idr + Status: To update + Tool usage (5 years) (usegalaxy.eu): 109 + Tool usage (5 years) (usegalaxy.org): 199 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 308 + Tool usage (all time) (usegalaxy.eu): 114 + Tool usage (all time) (usegalaxy.org): 199 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 313 + ToolShed categories: + - Sequence Analysis + ToolShed id: idr + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: omero-py + Conda version: 5.11.1 + Date of first commit of the suite: '2020-05-15' + Description: Image Data Resource downloading tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - idr_download_by_ids + Galaxy wrapper id: idr_download + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download + Galaxy wrapper version: '0.45' + No. of tool users (5 years) (usegalaxy.eu): 404 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 24 + No. of tool users (5 years) - all main servers: 428 + No. of tool users (all time) (usegalaxy.eu): 404 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 24 + No. of tool users (all time) - all main servers: 428 + Source: https://idr.openmicroscopy.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 37 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 38 + Tool usage (all time) (usegalaxy.eu): 37 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 38 + ToolShed categories: + - Data Source + ToolShed id: idr_download_by_ids + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2020-02-26' + Description: Get epitope binding predictions from IEDB-API + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - iedb_api + Galaxy wrapper id: iedb_api + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api + Galaxy wrapper version: 2.15.2 + No. of tool users (5 years) (usegalaxy.eu): 1539 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1539 + No. of tool users (all time) (usegalaxy.eu): 1539 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1539 + Source: http://tools.immuneepitope.org/main/tools-api/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 35 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 35 + Tool usage (all time) (usegalaxy.eu): 35 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 35 + ToolShed categories: + - Data Source + - Sequence Analysis + ToolShed id: iedb_api + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-infercnv + Conda version: 1.20.0 + Date of first commit of the suite: '2024-07-23' + Description: Infer Copy Number Variation from Single-Cell RNA-Seq Data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - infercnv + Galaxy wrapper id: infercnv + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv + Galaxy wrapper version: 1.20.0 + No. of tool users (5 years) (usegalaxy.eu): 10 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 10 + No. of tool users (all time) (usegalaxy.eu): 10 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 10 + Source: https://github.com/broadinstitute/infercnv + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Transcriptomics + - Variant Analysis + ToolShed id: infercnv + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: instrain + Conda version: 1.9.0 + Date of first commit of the suite: '2021-08-11' + Description: InStrain is a tool for analysis of co-occurring genome populations + from metagenomes + EDAM operation: + - SNP detection + - Genome comparison + EDAM operation (no superclasses): + - SNP detection + - Genome comparison + EDAM topic: + - Mapping + - Metagenomics + EDAM topic (no superclasses): + - Mapping + - Metagenomics + Galaxy tool ids: + - instrain_compare + - instrain_profile + Galaxy wrapper id: instrain + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain + Galaxy wrapper version: 1.5.3 + No. of tool users (5 years) (usegalaxy.eu): 102 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 102 + No. of tool users (all time) (usegalaxy.eu): 102 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 102 + Source: https://instrain.readthedocs.io/en/latest/# + Status: To update + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 16 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 16 + ToolShed categories: + - Metagenomics + ToolShed id: instrain + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + biii: null + bio.tool description: InStrain is a tool for analysis of co-occurring genome populations + from metagenomes that allows highly accurate genome comparisons, analysis of coverage, + microdiversity, and linkage, and sensitive SNP detection with gene localization + and synonymous non-synonymous identification + bio.tool id: instrain + bio.tool ids: + - instrain + bio.tool name: InStrain +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: integron_finder + Conda version: 2.0.5 + Date of first commit of the suite: '2022-09-22' + Description: '"IntegronFinder identify integrons with high accuracy and sensitivity.It + searches for attC sites using covariance models, for integron-integrases using + HMM profiles, and for other features (promoters, attI site) using pattern matching"' + EDAM operation: + - Nucleic acid feature detection + - Sequence motif recognition + - Protein feature detection + - Genome annotation + EDAM operation (no superclasses): + - Nucleic acid feature detection + - Sequence motif recognition + - Protein feature detection + - Genome annotation + EDAM topic: + - Functional genomics + - Mobile genetic elements + - Molecular biology + - Sequence analysis + EDAM topic (no superclasses): + - Functional genomics + - Mobile genetic elements + - Molecular biology + - Sequence analysis + Galaxy tool ids: + - integron_finder + Galaxy wrapper id: integron_finder + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder + Galaxy wrapper version: 2.0.5 + No. of tool users (5 years) (usegalaxy.eu): 55149 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 6085 + No. of tool users (5 years) - all main servers: 61234 + No. of tool users (all time) (usegalaxy.eu): 55149 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 6085 + No. of tool users (all time) - all main servers: 61234 + Source: https://github.com/gem-pasteur/Integron_Finder + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 161 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 73 + Tool usage (5 years) - all main servers: 234 + Tool usage (all time) (usegalaxy.eu): 161 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 73 + Tool usage (all time) - all main servers: 234 + ToolShed categories: + - Sequence Analysis + ToolShed id: integronfinder + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool to detect Integron in DNA sequences. + bio.tool id: integron_finder + bio.tool ids: + - integron_finder + bio.tool name: Integron Finder +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: coreutils + Conda version: '8.25' + Date of first commit of the suite: '2018-07-01' + Description: InterMine Exporter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - galaxy_intermine_exchange + Galaxy wrapper id: intermine_galaxy_exchange + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 37 + No. of tool users (5 years) (usegalaxy.org): 72 + No. of tool users (5 years) (usegalaxy.org.au): 108 + No. of tool users (5 years) - all main servers: 217 + No. of tool users (all time) (usegalaxy.eu): 46 + No. of tool users (all time) (usegalaxy.org): 87 + No. of tool users (all time) (usegalaxy.org.au): 108 + No. of tool users (all time) - all main servers: 241 + Source: https://github.com/intermine + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 13 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 20 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 15 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 28 + ToolShed categories: + - Convert Formats + ToolShed id: intermine_galaxy_exchange + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: interproscan + Conda version: 5.59_91.0 + Date of first commit of the suite: '2021-11-15' + Description: Interproscan queries the interpro database and provides annotations. + EDAM operation: + - Sequence motif recognition + - Protein feature detection + EDAM operation (no superclasses): + - Sequence motif recognition + - Protein feature detection + EDAM topic: + - Gene and protein families + - Sequence analysis + EDAM topic (no superclasses): + - Gene and protein families + - Sequence analysis + Galaxy tool ids: + - interproscan + Galaxy wrapper id: interproscan + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan + Galaxy wrapper version: 5.59-91.0 + No. of tool users (5 years) (usegalaxy.eu): 34689 + No. of tool users (5 years) (usegalaxy.org): 65 + No. of tool users (5 years) (usegalaxy.org.au): 10897 + No. of tool users (5 years) - all main servers: 45651 + No. of tool users (all time) (usegalaxy.eu): 55189 + No. of tool users (all time) (usegalaxy.org): 65 + No. of tool users (all time) (usegalaxy.org.au): 10897 + No. of tool users (all time) - all main servers: 66151 + Source: http://www.ebi.ac.uk/Tools/pfa/iprscan5/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1634 + Tool usage (5 years) (usegalaxy.org): 15 + Tool usage (5 years) (usegalaxy.org.au): 607 + Tool usage (5 years) - all main servers: 2256 + Tool usage (all time) (usegalaxy.eu): 1713 + Tool usage (all time) (usegalaxy.org): 15 + Tool usage (all time) (usegalaxy.org.au): 607 + Tool usage (all time) - all main servers: 2335 + ToolShed categories: + - Sequence Analysis + ToolShed id: interproscan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Scan sequences against the InterPro protein signature databases. + bio.tool id: interproscan_ebi + bio.tool ids: + - interproscan_ebi + bio.tool name: InterProScan (EBI) +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bx-python + Conda version: 0.13.0 + Date of first commit of the suite: '2020-07-14' + Description: Extract MAF blocks given a set of intervals + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - Interval2Maf1 + Galaxy wrapper id: interval2maf + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ + Galaxy wrapper version: 1.0.1+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 32 + No. of tool users (5 years) (usegalaxy.org): 758 + No. of tool users (5 years) (usegalaxy.org.au): 16 + No. of tool users (5 years) - all main servers: 806 + No. of tool users (all time) (usegalaxy.eu): 107 + No. of tool users (all time) (usegalaxy.org): 19538 + No. of tool users (all time) (usegalaxy.org.au): 24 + No. of tool users (all time) - all main servers: 19669 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 87 + Tool usage (5 years) (usegalaxy.org.au): 2 + Tool usage (5 years) - all main servers: 96 + Tool usage (all time) (usegalaxy.eu): 10 + Tool usage (all time) (usegalaxy.org): 1246 + Tool usage (all time) (usegalaxy.org.au): 2 + Tool usage (all time) - all main servers: 1258 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: interval2maf + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 1 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 1 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 1 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Tools for manipulating biological data, particularly multiple + sequence alignments. + bio.tool id: bx-python + bio.tool ids: + - bx-python + bio.tool name: bx-python +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: intervene + Conda version: 0.6.5 + Date of first commit of the suite: '2018-09-11' + Description: Create pairwise and upset plots + EDAM operation: + - Sequence comparison + - Sequence visualisation + EDAM operation (no superclasses): + - Sequence comparison + - Sequence visualisation + EDAM topic: + - Computational biology + EDAM topic (no superclasses): + - Computational biology + Galaxy tool ids: + - intervene_pairwise + - intervene_upset + Galaxy wrapper id: intervene + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene + Galaxy wrapper version: 0.6.5 + No. of tool users (5 years) (usegalaxy.eu): 1557 + No. of tool users (5 years) (usegalaxy.org): 4458 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6015 + No. of tool users (all time) (usegalaxy.eu): 1607 + No. of tool users (all time) (usegalaxy.org): 4458 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6065 + Source: https://intervene.readthedocs.io + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 278 + Tool usage (5 years) (usegalaxy.org): 458 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 736 + Tool usage (all time) (usegalaxy.eu): 292 + Tool usage (all time) (usegalaxy.org): 458 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 750 + ToolShed categories: + - Statistics + ToolShed id: intervene + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: 'Tool for intersection and visualization of multiple gene + or genomic region sets. Intervene contains three modules: venn to generate Venn + diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and + pairwise to compute and visualize intersections of multiple sets as clustered + heat maps.' + bio.tool id: intervene + bio.tool ids: + - intervene + bio.tool name: Intervene +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: iqtree + Conda version: 2.3.6 + Date of first commit of the suite: '2017-11-15' + Description: Efficient phylogenomic software by maximum likelihood + EDAM operation: + - Phylogenetic analysis + - Sequence analysis + EDAM operation (no superclasses): + - Phylogenetic analysis + - Sequence analysis + EDAM topic: + - Phylogenetics + EDAM topic (no superclasses): + - Phylogenetics + Galaxy tool ids: + - iqtree + Galaxy wrapper id: iqtree + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ + Galaxy wrapper version: 2.3.6 + No. of tool users (5 years) (usegalaxy.eu): 28279 + No. of tool users (5 years) (usegalaxy.org): 24662 + No. of tool users (5 years) (usegalaxy.org.au): 9780 + No. of tool users (5 years) - all main servers: 62721 + No. of tool users (all time) (usegalaxy.eu): 28481 + No. of tool users (all time) (usegalaxy.org): 24662 + No. of tool users (all time) (usegalaxy.org.au): 10086 + No. of tool users (all time) - all main servers: 63229 + Source: http://www.iqtree.org/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1623 + Tool usage (5 years) (usegalaxy.org): 2093 + Tool usage (5 years) (usegalaxy.org.au): 979 + Tool usage (5 years) - all main servers: 4695 + Tool usage (all time) (usegalaxy.eu): 1646 + Tool usage (all time) (usegalaxy.org): 2093 + Tool usage (all time) (usegalaxy.org.au): 992 + Tool usage (all time) - all main servers: 4731 + ToolShed categories: + - Phylogenetics + ToolShed id: iqtree + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A fast and effective stochastic algorithm to infer phylogenetic + trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in + terms of likelihoods with similar computing time + bio.tool id: iqtree + bio.tool ids: + - iqtree + bio.tool name: iqtree +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: samtools + Conda version: '1.21' + Date of first commit of the suite: '2021-01-17' + Description: Refine insertion sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - irissv + Galaxy wrapper id: irissv + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tools/irissv/ + Galaxy wrapper version: 1.0.5 + No. of tool users (5 years) (usegalaxy.eu): 29 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 29 + No. of tool users (all time) (usegalaxy.eu): 29 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 29 + Source: https://github.com/mkirsche/Iris + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Variant Analysis + ToolShed id: irissv + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: isescan + Conda version: 1.7.2.1 + Date of first commit of the suite: '2022-09-01' + Description: '"ISEScan is a pipeline to identify IS (Insertion Sequence) elements + in genome and metagenomebased on profile hidden Markov models constructed from + manually curated IS elements."' + EDAM operation: + - Structural variation detection + EDAM operation (no superclasses): + - Structural variation detection + EDAM topic: + - Genomics + - DNA structural variation + - Sequence analysis + - Genetic variation + EDAM topic (no superclasses): + - Genomics + - Sequence analysis + - Genetic variation + Galaxy tool ids: + - isescan + Galaxy wrapper id: isescan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan + Galaxy wrapper version: 1.7.2.3 + No. of tool users (5 years) (usegalaxy.eu): 59386 + No. of tool users (5 years) (usegalaxy.org): 56 + No. of tool users (5 years) (usegalaxy.org.au): 4741 + No. of tool users (5 years) - all main servers: 64183 + No. of tool users (all time) (usegalaxy.eu): 59386 + No. of tool users (all time) (usegalaxy.org): 56 + No. of tool users (all time) (usegalaxy.org.au): 4741 + No. of tool users (all time) - all main servers: 64183 + Source: https://github.com/xiezhq/ISEScan + Status: To update + Tool usage (5 years) (usegalaxy.eu): 151 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 59 + Tool usage (5 years) - all main servers: 211 + Tool usage (all time) (usegalaxy.eu): 151 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 59 + Tool usage (all time) - all main servers: 211 + ToolShed categories: + - Sequence Analysis + ToolShed id: ISEScan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Automated identification of insertion sequence elements in + prokaryotic genomes. + bio.tool id: ISEScan + bio.tool ids: + - ISEScan + bio.tool name: ISEScan +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-isoformswitchanalyzer + Conda version: 2.2.0 + Date of first commit of the suite: '2023-05-24' + Description: Statistical identification of isoform switching from RNA-seq derived + quantification of novel and/or annotated full-length isoforms. + EDAM operation: + - Sequence comparison + - Sequence analysis + EDAM operation (no superclasses): + - Sequence comparison + - Sequence analysis + EDAM topic: + - Computational biology + - Gene transcripts + EDAM topic (no superclasses): + - Computational biology + - Gene transcripts + Galaxy tool ids: + - isoformswitchanalyzer + Galaxy wrapper id: isoformswitchanalyzer + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer + Galaxy wrapper version: 1.20.0 + No. of tool users (5 years) (usegalaxy.eu): 1301 + No. of tool users (5 years) (usegalaxy.org): 1331 + No. of tool users (5 years) (usegalaxy.org.au): 507 + No. of tool users (5 years) - all main servers: 3139 + No. of tool users (all time) (usegalaxy.eu): 1301 + No. of tool users (all time) (usegalaxy.org): 1331 + No. of tool users (all time) (usegalaxy.org.au): 507 + No. of tool users (all time) - all main servers: 3139 + Source: https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 59 + Tool usage (5 years) (usegalaxy.org): 60 + Tool usage (5 years) (usegalaxy.org.au): 9 + Tool usage (5 years) - all main servers: 128 + Tool usage (all time) (usegalaxy.eu): 59 + Tool usage (all time) (usegalaxy.org): 60 + Tool usage (all time) (usegalaxy.org.au): 9 + Tool usage (all time) - all main servers: 128 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: isoformswitchanalyzer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Enables identification of isoform switches with predicted + functional consequences from RNA-seq data. Consequences can be chosen from a long + list but includes protein domains gain/loss changes in NMD sensitivity etc. It + directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and + RSEM but other transcript qunatification tools are easy to import as well. + bio.tool id: IsoformSwitchAnalyzeR + bio.tool ids: + - IsoformSwitchAnalyzeR + bio.tool name: IsoformSwitchAnalyzeR +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: ivar + Conda version: 1.4.3 + Date of first commit of the suite: '2020-06-05' + Description: iVar is a computational package that contains functions broadly useful + for viral amplicon-based sequencing + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ivar_consensus + - ivar_filtervariants + - ivar_removereads + - ivar_trim + - ivar_variants + Galaxy wrapper id: ivar + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ + Galaxy wrapper version: 1.4.3 + No. of tool users (5 years) (usegalaxy.eu): 1252220 + No. of tool users (5 years) (usegalaxy.org): 126027 + No. of tool users (5 years) (usegalaxy.org.au): 41901 + No. of tool users (5 years) - all main servers: 1420148 + No. of tool users (all time) (usegalaxy.eu): 1252220 + No. of tool users (all time) (usegalaxy.org): 126027 + No. of tool users (all time) (usegalaxy.org.au): 41901 + No. of tool users (all time) - all main servers: 1420148 + Source: https://github.com/andersen-lab/ivar + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2366 + Tool usage (5 years) (usegalaxy.org): 2496 + Tool usage (5 years) (usegalaxy.org.au): 993 + Tool usage (5 years) - all main servers: 5855 + Tool usage (all time) (usegalaxy.eu): 2366 + Tool usage (all time) (usegalaxy.org): 2496 + Tool usage (all time) (usegalaxy.org.au): 993 + Tool usage (all time) - all main servers: 5855 + ToolShed categories: + - Sequence Analysis + ToolShed id: ivar + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 5 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 4 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 4 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 4 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: bioconductor-iwtomics + Conda version: 1.26.0 + Date of first commit of the suite: '2017-06-08' + Description: Interval-Wise Testing for Omics Data + EDAM operation: + - Differential gene expression analysis + - Differentially-methylated region identification + - Peak calling + - Genome annotation + - Comparison + EDAM operation (no superclasses): + - Differential gene expression analysis + - Peak calling + - Genome annotation + - Comparison + EDAM topic: + - Statistics and probability + EDAM topic (no superclasses): + - Statistics and probability + Galaxy tool ids: + - iwtomics_loadandplot + - iwtomics_plotwithscale + - iwtomics_testandplot + Galaxy wrapper id: iwtomics + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 675 + No. of tool users (5 years) (usegalaxy.org): 159 + No. of tool users (5 years) (usegalaxy.org.au): 383 + No. of tool users (5 years) - all main servers: 1217 + No. of tool users (all time) (usegalaxy.eu): 690 + No. of tool users (all time) (usegalaxy.org): 251 + No. of tool users (all time) (usegalaxy.org.au): 383 + No. of tool users (all time) - all main servers: 1324 + Source: https://bioconductor.org/packages/release/bioc/html/IWTomics.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 27 + Tool usage (5 years) (usegalaxy.org): 29 + Tool usage (5 years) (usegalaxy.org.au): 12 + Tool usage (5 years) - all main servers: 68 + Tool usage (all time) (usegalaxy.eu): 28 + Tool usage (all time) (usegalaxy.org): 49 + Tool usage (all time) (usegalaxy.org.au): 12 + Tool usage (all time) - all main servers: 89 + ToolShed categories: + - Statistics + ToolShed id: iwtomics + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: Implementation of the Interval-Wise Testing (IWT) for omics + data. This inferential procedure tests for differences in "Omics" data between + two groups of genomic regions (or between a group of genomic regions and a reference + center of symmetry), and does not require fixing location and scale at the outset. + bio.tool id: iwtomics + bio.tool ids: + - iwtomics + bio.tool name: IWTomics +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: jasminesv + Conda version: 1.1.5 + Date of first commit of the suite: '2021-01-17' + Description: Merge structural variants across samples + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - jasminesv + Galaxy wrapper id: jasminesv + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/jasminesv/ + Galaxy wrapper version: 1.0.11 + No. of tool users (5 years) (usegalaxy.eu): 32 + No. of tool users (5 years) (usegalaxy.org): 53 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 85 + No. of tool users (all time) (usegalaxy.eu): 32 + No. of tool users (all time) (usegalaxy.org): 53 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 85 + Source: https://github.com/mkirsche/Jasmine/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 19 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 28 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 19 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 28 + ToolShed categories: + - Variant Analysis + ToolShed id: jasminesv + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: jbrowse + Conda version: 1.16.11 + Date of first commit of the suite: '2019-08-29' + Description: JBrowse Genome Browser integrated as a Galaxy Tool + EDAM operation: + - Genome visualisation + EDAM operation (no superclasses): + - Genome visualisation + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - jbrowse_to_standalone + - jbrowse + Galaxy wrapper id: jbrowse + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse + Galaxy wrapper version: 1.16.11 + No. of tool users (5 years) (usegalaxy.eu): 21153 + No. of tool users (5 years) (usegalaxy.org): 17428 + No. of tool users (5 years) (usegalaxy.org.au): 15673 + No. of tool users (5 years) - all main servers: 54254 + No. of tool users (all time) (usegalaxy.eu): 22174 + No. of tool users (all time) (usegalaxy.org): 17428 + No. of tool users (all time) (usegalaxy.org.au): 17267 + No. of tool users (all time) - all main servers: 56869 + Source: https://jbrowse.org + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 5514 + Tool usage (5 years) (usegalaxy.org): 6458 + Tool usage (5 years) (usegalaxy.org.au): 3248 + Tool usage (5 years) - all main servers: 15220 + Tool usage (all time) (usegalaxy.eu): 5779 + Tool usage (all time) (usegalaxy.org): 6458 + Tool usage (all time) (usegalaxy.org.au): 3786 + Tool usage (all time) - all main servers: 16023 + ToolShed categories: + - Sequence Analysis + ToolShed id: jbrowse + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Slick, speedy genome browser with a responsive and dynamic + AJAX interface for visualization of genome data. Being developed by the GMOD project + as a successor to GBrowse. + bio.tool id: jbrowse + bio.tool ids: + - jbrowse + bio.tool name: JBrowse +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: jcvi + Conda version: 1.4.16 + Date of first commit of the suite: '2018-07-31' + Description: Compute statistics from a genome annotation in GFF3 format (using JCVI + Python utilities) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - jcvi_gff_stats + Galaxy wrapper id: jcvi_gff_stats + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats + Galaxy wrapper version: 0.8.4 + No. of tool users (5 years) (usegalaxy.eu): 2747 + No. of tool users (5 years) (usegalaxy.org): 2311 + No. of tool users (5 years) (usegalaxy.org.au): 1145 + No. of tool users (5 years) - all main servers: 6203 + No. of tool users (all time) (usegalaxy.eu): 2926 + No. of tool users (all time) (usegalaxy.org): 2311 + No. of tool users (all time) (usegalaxy.org.au): 1145 + No. of tool users (all time) - all main servers: 6382 + Source: https://github.com/tanghaibao/jcvi + Status: To update + Tool usage (5 years) (usegalaxy.eu): 596 + Tool usage (5 years) (usegalaxy.org): 741 + Tool usage (5 years) (usegalaxy.org.au): 469 + Tool usage (5 years) - all main servers: 1806 + Tool usage (all time) (usegalaxy.eu): 637 + Tool usage (all time) (usegalaxy.org): 741 + Tool usage (all time) (usegalaxy.org.au): 469 + Tool usage (all time) - all main servers: 1847 + ToolShed categories: + - Sequence Analysis + ToolShed id: jcvi_gff_stats + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: kmer-jellyfish + Conda version: 2.3.1 + Date of first commit of the suite: '2021-04-07' + Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in + DNA + EDAM operation: + - k-mer counting + EDAM operation (no superclasses): + - k-mer counting + EDAM topic: + - Sequence analysis + - Genomics + EDAM topic (no superclasses): + - Sequence analysis + - Genomics + Galaxy tool ids: + - jellyfish + Galaxy wrapper id: jellyfish + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 1825 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 971 + No. of tool users (5 years) - all main servers: 2796 + No. of tool users (all time) (usegalaxy.eu): 1825 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 971 + No. of tool users (all time) - all main servers: 2796 + Source: https://github.com/gmarcais/Jellyfish + Status: To update + Tool usage (5 years) (usegalaxy.eu): 237 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 56 + Tool usage (5 years) - all main servers: 293 + Tool usage (all time) (usegalaxy.eu): 237 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 56 + Tool usage (all time) - all main servers: 293 + ToolShed categories: + - Assembly + ToolShed id: jellyfish + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A command-line algorithm for counting k-mers in DNA sequence. + bio.tool id: Jellyfish + bio.tool ids: + - Jellyfish + bio.tool name: Jellyfish +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-data.table + Conda version: 1.11.6 + Date of first commit of the suite: '2017-05-31' + Description: This tool will join datasets according to a column with identifier + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - join_files_by_id + Galaxy wrapper id: join_files_by_id + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Text Manipulation + ToolShed id: join_files_by_id + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: jq + Conda version: '1.5' + Date of first commit of the suite: '2017-06-22' + Description: JQ is a lightweight and flexible command-line JSON processor + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - jq + Galaxy wrapper id: jq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 660 + No. of tool users (5 years) (usegalaxy.org): 336 + No. of tool users (5 years) (usegalaxy.org.au): 281 + No. of tool users (5 years) - all main servers: 1277 + No. of tool users (all time) (usegalaxy.eu): 2374 + No. of tool users (all time) (usegalaxy.org): 336 + No. of tool users (all time) (usegalaxy.org.au): 281 + No. of tool users (all time) - all main servers: 2991 + Source: https://stedolan.github.io/jq/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 61 + Tool usage (5 years) (usegalaxy.org): 82 + Tool usage (5 years) (usegalaxy.org.au): 11 + Tool usage (5 years) - all main servers: 154 + Tool usage (all time) (usegalaxy.eu): 63 + Tool usage (all time) (usegalaxy.org): 82 + Tool usage (all time) (usegalaxy.org.au): 11 + Tool usage (all time) - all main servers: 156 + ToolShed categories: + - Text Manipulation + ToolShed id: jq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: jvarkit-wgscoverageplotter + Conda version: '20201223' + Date of first commit of the suite: '2021-02-11' + Description: 'Jvarkit : Java utilities for Bioinformatics' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - jvarkit_wgscoverageplotter + Galaxy wrapper id: jvarkit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit + Galaxy wrapper source: https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit + Galaxy wrapper version: '20201223' + No. of tool users (5 years) (usegalaxy.eu): 7179 + No. of tool users (5 years) (usegalaxy.org): 11138 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 18317 + No. of tool users (all time) (usegalaxy.eu): 7179 + No. of tool users (all time) (usegalaxy.org): 11138 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 18317 + Source: https://lindenb.github.io/jvarkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 509 + Tool usage (5 years) (usegalaxy.org): 1145 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1654 + Tool usage (all time) (usegalaxy.eu): 509 + Tool usage (all time) (usegalaxy.org): 1145 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1654 + ToolShed categories: + - SAM + ToolShed id: jvarkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: kallisto + Conda version: 0.51.1 + Date of first commit of the suite: '2017-08-09' + Description: kallisto is a program for quantifying abundances of transcripts from + RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. + It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility + of reads with targets, without the need foralignment. + EDAM operation: + - Gene expression profiling + EDAM operation (no superclasses): + - Gene expression profiling + EDAM topic: + - Transcriptomics + - RNA-seq + - Gene expression + EDAM topic (no superclasses): + - Transcriptomics + Galaxy tool ids: + - kallisto_pseudo + - kallisto_quant + Galaxy wrapper id: kallisto + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ + Galaxy wrapper version: 0.48.0 + No. of tool users (5 years) (usegalaxy.eu): 28398 + No. of tool users (5 years) (usegalaxy.org): 73705 + No. of tool users (5 years) (usegalaxy.org.au): 5333 + No. of tool users (5 years) - all main servers: 107436 + No. of tool users (all time) (usegalaxy.eu): 29031 + No. of tool users (all time) (usegalaxy.org): 80087 + No. of tool users (all time) (usegalaxy.org.au): 5567 + No. of tool users (all time) - all main servers: 114685 + Source: https://pachterlab.github.io/kallisto/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 932 + Tool usage (5 years) (usegalaxy.org): 2603 + Tool usage (5 years) (usegalaxy.org.au): 218 + Tool usage (5 years) - all main servers: 3753 + Tool usage (all time) (usegalaxy.eu): 965 + Tool usage (all time) (usegalaxy.org): 3025 + Tool usage (all time) (usegalaxy.org.au): 230 + Tool usage (all time) - all main servers: 4220 + ToolShed categories: + - Transcriptomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: A program for quantifying abundances of transcripts from RNA-Seq + data, or more generally of target sequences using high-throughput sequencing reads. + It is based on the novel idea of pseudoalignment for rapidly determining the compatibility + of reads with targets, without the need for alignment. + bio.tool id: kallisto + bio.tool ids: + - kallisto + bio.tool name: kallisto +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: kcalign + Conda version: 1.0.2 + Date of first commit of the suite: '2020-02-20' + Description: Kc-Align custom tool + EDAM operation: + - Multiple sequence alignment + EDAM operation (no superclasses): + - Multiple sequence alignment + EDAM topic: + - Mapping + EDAM topic (no superclasses): + - Mapping + Galaxy tool ids: + - kc-align + Galaxy wrapper id: kc-align + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 379 + No. of tool users (5 years) (usegalaxy.org): 8259 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 8638 + No. of tool users (all time) (usegalaxy.eu): 379 + No. of tool users (all time) (usegalaxy.org): 8259 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8638 + Source: https://github.com/davebx/kc-align + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 53 + Tool usage (5 years) (usegalaxy.org): 271 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 324 + Tool usage (all time) (usegalaxy.eu): 53 + Tool usage (all time) (usegalaxy.org): 271 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 324 + ToolShed categories: + - Sequence Analysis + ToolShed id: kc_align + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A fast and accurate tool for performing codon-aware multiple + sequence alignments + bio.tool id: kc-align + bio.tool ids: + - kc-align + bio.tool name: kc-align +- Available on UseGalaxy.eu: 8 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 8 + Available on UseGalaxy.org.au: 8 + Conda id: khmer + Conda version: 3.0.0a3 + Date of first commit of the suite: '2015-11-08' + Description: In-memory nucleotide sequence k-mer counting, filtering, graph traversal + and more + EDAM operation: + - Standardisation and normalisation + - De-novo assembly + EDAM operation (no superclasses): + - Standardisation and normalisation + - De-novo assembly + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - khmer_abundance_distribution_single + - khmer_abundance_distribution + - khmer_count_median + - khmer_partition + - khmer_extract_partitions + - khmer_filter_abundance + - khmer_filter_below_abundance_cutoff + - khmer_normalize_by_median + Galaxy wrapper id: khmer + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer + Galaxy wrapper version: 3.0.0a3 + No. of tool users (5 years) (usegalaxy.eu): 1995 + No. of tool users (5 years) (usegalaxy.org): 1430 + No. of tool users (5 years) (usegalaxy.org.au): 1580 + No. of tool users (5 years) - all main servers: 5005 + No. of tool users (all time) (usegalaxy.eu): 2091 + No. of tool users (all time) (usegalaxy.org): 1430 + No. of tool users (all time) (usegalaxy.org.au): 1580 + No. of tool users (all time) - all main servers: 5101 + Source: https://khmer.readthedocs.org/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 174 + Tool usage (5 years) (usegalaxy.org): 389 + Tool usage (5 years) (usegalaxy.org.au): 56 + Tool usage (5 years) - all main servers: 619 + Tool usage (all time) (usegalaxy.eu): 193 + Tool usage (all time) (usegalaxy.org): 389 + Tool usage (all time) (usegalaxy.org.au): 56 + Tool usage (all time) - all main servers: 638 + ToolShed categories: + - Assembly + - Next Gen Mappers + ToolShed id: khmer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 8 + Tools available on UseGalaxy.cz: 8 + Tools available on UseGalaxy.eu: 8 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 8 + Tools available on UseGalaxy.org (Main): 8 + Tools available on UseGalaxy.org.au: 8 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 8 + UseGalaxy.cz: 8 + UseGalaxy.eu: 8 + UseGalaxy.fr: 1 + UseGalaxy.no: 8 + UseGalaxy.or: 8 + biii: null + bio.tool description: khmer is a set of command-line tools for working with DNA + shotgun sequencing data from genomes, transcriptomes, metagenomes, and single + cells. khmer can make de novo assemblies faster, and sometimes better. khmer can + also identify (and fix) problems with shotgun data. + bio.tool id: khmer + bio.tool ids: + - khmer + bio.tool name: khmer +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: king + Conda version: 2.2.7 + Date of first commit of the suite: '2021-11-16' + Description: Kinship-based INference for Gwas + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - king + Galaxy wrapper id: king + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/king + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ + Galaxy wrapper version: 2.2.7 + No. of tool users (5 years) (usegalaxy.eu): 8 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 8 + No. of tool users (all time) (usegalaxy.eu): 8 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8 + Source: http://people.virginia.edu/~wc9c/KING/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Variant Analysis + ToolShed id: king + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: kleborate + Conda version: 3.1.0 + Date of first commit of the suite: '2022-09-09' + Description: Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella + pneumoniae species complex (KpSC) + EDAM operation: + - Multilocus sequence typing + - Genome assembly + - Virulence prediction + EDAM operation (no superclasses): + - Multilocus sequence typing + - Genome assembly + - Virulence prediction + EDAM topic: + - Public health and epidemiology + - Metagenomics + - Population genomics + - Sequence assembly + - Whole genome sequencing + EDAM topic (no superclasses): + - Public health and epidemiology + - Metagenomics + - Population genomics + - Sequence assembly + - Whole genome sequencing + Galaxy tool ids: + - kleborate + Galaxy wrapper id: kleborate + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate + Galaxy wrapper source: https://github.com/katholt/Kleborate + Galaxy wrapper version: 2.3.2 + No. of tool users (5 years) (usegalaxy.eu): 503 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 503 + No. of tool users (all time) (usegalaxy.eu): 503 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 503 + Source: https://github.com/katholt/Kleborate/wiki + Status: To update + Tool usage (5 years) (usegalaxy.eu): 58 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 58 + Tool usage (all time) (usegalaxy.eu): 58 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 58 + ToolShed categories: + - Metagenomics + ToolShed id: kleborate + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: 'Genomic surveillance framework and global population structure + for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella + pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript + describing the Kleborate software in full is currently in preparation. In the + meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic + surveillance framework and global population structure for Klebsiella pneumoniae. + bioRxiv (2020).' + bio.tool id: kleborate + bio.tool ids: + - kleborate + bio.tool name: Kleborate +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: kma + Conda version: 1.4.15 + Date of first commit of the suite: '2019-10-30' + Description: Map with KMA + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - kma_map + Galaxy wrapper id: kma + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma + Galaxy wrapper version: 1.4.14 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1 + Source: https://bitbucket.org/genomicepidemiology/kma + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Next Gen Mappers + ToolShed id: kma + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: kofamscan + Conda version: 1.3.0 + Date of first commit of the suite: '2020-11-12' + Description: Gene function annotation tool based on KEGG Orthology and hidden Markov + model + EDAM operation: + - Sequence analysis + - Gene functional annotation + EDAM operation (no superclasses): + - Sequence analysis + - Gene functional annotation + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - kofamscan + Galaxy wrapper id: kofamscan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan + Galaxy wrapper version: 1.3.0 + No. of tool users (5 years) (usegalaxy.eu): 1342 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1342 + No. of tool users (all time) (usegalaxy.eu): 1342 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1342 + Source: https://github.com/takaram/kofam_scan + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 63 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 63 + Tool usage (all time) (usegalaxy.eu): 63 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 63 + ToolShed categories: + - Sequence Analysis + ToolShed id: kofamscan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: KofamScan is a gene function annotation tool based on KEGG + Orthology and hidden Markov model. You need KOfam database to use this tool. + bio.tool id: kofamscan + bio.tool ids: + - kofamscan + bio.tool name: kofamscan +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: kraken-biom + Conda version: 1.2.0 + Date of first commit of the suite: '2022-09-03' + Description: Create BIOM-format tables (http://biom-format.org) from Kraken output + (http://ccb.jhu.edu/software/kraken/) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - kraken_biom + Galaxy wrapper id: kraken_biom + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom + Galaxy wrapper source: https://github.com/smdabdoub/kraken-biom + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 3185 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 385 + No. of tool users (5 years) - all main servers: 3570 + No. of tool users (all time) (usegalaxy.eu): 3185 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 385 + No. of tool users (all time) - all main servers: 3570 + Source: https://github.com/smdabdoub/kraken-biom + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 495 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 48 + Tool usage (5 years) - all main servers: 543 + Tool usage (all time) (usegalaxy.eu): 495 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 48 + Tool usage (all time) - all main servers: 543 + ToolShed categories: + - Metagenomics + ToolShed id: kraken_biom + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: biopython + Conda version: '1.70' + Date of first commit of the suite: '2016-06-01' + Description: Kraken taxonomy report + EDAM operation: + - Visualisation + - Classification + EDAM operation (no superclasses): + - Visualisation + - Classification + EDAM topic: + - Metagenomics + - Taxonomy + EDAM topic (no superclasses): + - Metagenomics + - Taxonomy + Galaxy tool ids: + - kraken_taxonomy_report + Galaxy wrapper id: kraken_taxonomy_report + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report + Galaxy wrapper version: 0.0.3 + No. of tool users (5 years) (usegalaxy.eu): 3981 + No. of tool users (5 years) (usegalaxy.org): 4087 + No. of tool users (5 years) (usegalaxy.org.au): 88 + No. of tool users (5 years) - all main servers: 8156 + No. of tool users (all time) (usegalaxy.eu): 3986 + No. of tool users (all time) (usegalaxy.org): 5610 + No. of tool users (all time) (usegalaxy.org.au): 88 + No. of tool users (all time) - all main servers: 9684 + Source: https://github.com/blankenberg/Kraken-Taxonomy-Report + Status: To update + Tool usage (5 years) (usegalaxy.eu): 769 + Tool usage (5 years) (usegalaxy.org): 991 + Tool usage (5 years) (usegalaxy.org.au): 41 + Tool usage (5 years) - all main servers: 1801 + Tool usage (all time) (usegalaxy.eu): 771 + Tool usage (all time) (usegalaxy.org): 1284 + Tool usage (all time) (usegalaxy.org.au): 41 + Tool usage (all time) - all main servers: 2096 + ToolShed categories: + - Metagenomics + ToolShed id: kraken_taxonomy_report + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: view report of classification for multiple samples + bio.tool id: Kraken-Taxonomy-Report + bio.tool ids: + - Kraken-Taxonomy-Report + bio.tool name: Kraken-Taxonomy-Report +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 6 + Available on UseGalaxy.org (Main): 6 + Available on UseGalaxy.org.au: 6 + Conda id: krakentools + Conda version: '1.2' + Date of first commit of the suite: '2023-01-13' + Description: KrakenTools is a suite of scripts to be used alongside the Kraken + EDAM operation: + - Visualisation + - Aggregation + EDAM operation (no superclasses): + - Visualisation + - Aggregation + EDAM topic: + - Taxonomy + - Metagenomics + EDAM topic (no superclasses): + - Taxonomy + - Metagenomics + Galaxy tool ids: + - krakentools_alpha_diversity + - krakentools_beta_diversity + - krakentools_combine_kreports + - krakentools_extract_kraken_reads + - krakentools_kreport2krona + - krakentools_kreport2mpa + Galaxy wrapper id: krakentools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools + Galaxy wrapper version: '1.2' + No. of tool users (5 years) (usegalaxy.eu): 48516 + No. of tool users (5 years) (usegalaxy.org): 8787 + No. of tool users (5 years) (usegalaxy.org.au): 4369 + No. of tool users (5 years) - all main servers: 61672 + No. of tool users (all time) (usegalaxy.eu): 48516 + No. of tool users (all time) (usegalaxy.org): 8787 + No. of tool users (all time) (usegalaxy.org.au): 4369 + No. of tool users (all time) - all main servers: 61672 + Source: https://github.com/jenniferlu717/KrakenTools + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2373 + Tool usage (5 years) (usegalaxy.org): 943 + Tool usage (5 years) (usegalaxy.org.au): 393 + Tool usage (5 years) - all main servers: 3709 + Tool usage (all time) (usegalaxy.eu): 2373 + Tool usage (all time) (usegalaxy.org): 943 + Tool usage (all time) (usegalaxy.org.au): 393 + Tool usage (all time) - all main servers: 3709 + ToolShed categories: + - Metagenomics + ToolShed id: krakentools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 6 + Tools available on GalaxyTrakr: 6 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 6 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 6 + Tools available on UseGalaxy.org.au: 6 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.fr: 6 + UseGalaxy.or: 6 + biii: null + bio.tool description: KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq + output files + bio.tool id: krakentools + bio.tool ids: + - krakentools + bio.tool name: KrakenTools +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: krocus + Conda version: 1.0.3 + Date of first commit of the suite: '2019-09-03' + Description: Predict MLST directly from uncorrected long reads + EDAM operation: + - Multilocus sequence typing + - k-mer counting + EDAM operation (no superclasses): + - Multilocus sequence typing + - k-mer counting + EDAM topic: + - Public health and epidemiology + EDAM topic (no superclasses): + - Public health and epidemiology + Galaxy tool ids: + - krocus + Galaxy wrapper id: krocus + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/quadram-institute-bioscience/krocus + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: krocus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Predict MLST directly from uncorrected long reads + bio.tool id: krocus + bio.tool ids: + - krocus + bio.tool name: krocus +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: last + Conda version: '1584' + Date of first commit of the suite: '2020-06-17' + Description: LAST finds similar regions between sequences. + EDAM operation: + - Sequence alignment + EDAM operation (no superclasses): + - Sequence alignment + EDAM topic: + - Genomics + - Comparative genomics + EDAM topic (no superclasses): + - Comparative genomics + Galaxy tool ids: + - last_al + - last_db + - last_split + - last_train + - last_maf_convert + Galaxy wrapper id: last + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/last + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/last + Galaxy wrapper version: '1205' + No. of tool users (5 years) (usegalaxy.eu): 329 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 329 + No. of tool users (all time) (usegalaxy.eu): 329 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 329 + Source: http://last.cbrc.jp/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 94 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 94 + Tool usage (all time) (usegalaxy.eu): 94 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 94 + ToolShed categories: + - Sequence Analysis + ToolShed id: last + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.no: 5 + biii: null + bio.tool description: Short read alignment program incorporating quality scores + bio.tool id: last + bio.tool ids: + - last + bio.tool name: LAST +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: lastz + Conda version: 1.04.22 + Date of first commit of the suite: '2018-02-19' + Description: Galaxy wrappers for the Lastz and Lastz_d + EDAM operation: + - Sequence alignment + - Read mapping + EDAM operation (no superclasses): + - Sequence alignment + - Read mapping + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - lastz_wrapper_2 + - lastz_d_wrapper + Galaxy wrapper id: lastz + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz + Galaxy wrapper version: 1.04.22 + No. of tool users (5 years) (usegalaxy.eu): 77409 + No. of tool users (5 years) (usegalaxy.org): 156658 + No. of tool users (5 years) (usegalaxy.org.au): 38579 + No. of tool users (5 years) - all main servers: 272646 + No. of tool users (all time) (usegalaxy.eu): 84356 + No. of tool users (all time) (usegalaxy.org): 193590 + No. of tool users (all time) (usegalaxy.org.au): 38780 + No. of tool users (all time) - all main servers: 316726 + Source: https://github.com/lastz/lastz + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 447 + Tool usage (5 years) (usegalaxy.org): 870 + Tool usage (5 years) (usegalaxy.org.au): 173 + Tool usage (5 years) - all main servers: 1490 + Tool usage (all time) (usegalaxy.eu): 475 + Tool usage (all time) (usegalaxy.org): 3511 + Tool usage (all time) (usegalaxy.org.au): 203 + Tool usage (all time) - all main servers: 4189 + ToolShed categories: + - Next Gen Mappers + ToolShed id: lastz + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: A tool for (1) aligning two DNA sequences, and (2) inferring + appropriate scoring parameters automatically. + bio.tool id: lastz + bio.tool ids: + - lastz + bio.tool name: LASTZ +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: lcr_genie + Conda version: null + Date of first commit of the suite: '2022-12-02' + Description: Ligase Chain Reaction Genie + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - lcrgenie + Galaxy wrapper id: lcrgenie + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/neilswainston/LCRGenie + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: lcrgenie + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: legsta + Conda version: 0.5.1 + Date of first commit of the suite: '2022-02-21' + Description: Performs in silico Legionella pneumophila sequence based typing. + EDAM operation: + - Sequence analysis + EDAM operation (no superclasses): + - Sequence analysis + EDAM topic: + - Public health and epidemiology + EDAM topic (no superclasses): + - Public health and epidemiology + Galaxy tool ids: + - legsta + Galaxy wrapper id: legsta + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta + Galaxy wrapper source: https://github.com/tseemann/legsta + Galaxy wrapper version: 0.5.1 + No. of tool users (5 years) (usegalaxy.eu): 92 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 92 + No. of tool users (all time) (usegalaxy.eu): 92 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 92 + Source: https://github.com/tseemann/legsta + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Sequence Analysis + ToolShed id: legsta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Performs in silico Legionella pneumophila sequence based typing + bio.tool id: legsta + bio.tool ids: + - legsta + bio.tool name: legsta +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-optparse + Conda version: 1.3.2 + Date of first commit of the suite: '2016-11-13' + Description: Gets gene length and gc content from a fasta and a GTF file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - length_and_gc_content + Galaxy wrapper id: length_and_gc_content + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 4349 + No. of tool users (5 years) (usegalaxy.org): 2093 + No. of tool users (5 years) (usegalaxy.org.au): 201 + No. of tool users (5 years) - all main servers: 6643 + No. of tool users (all time) (usegalaxy.eu): 4466 + No. of tool users (all time) (usegalaxy.org): 2286 + No. of tool users (all time) (usegalaxy.org.au): 201 + No. of tool users (all time) - all main servers: 6953 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content + Status: To update + Tool usage (5 years) (usegalaxy.eu): 666 + Tool usage (5 years) (usegalaxy.org): 928 + Tool usage (5 years) (usegalaxy.org.au): 77 + Tool usage (5 years) - all main servers: 1671 + Tool usage (all time) (usegalaxy.eu): 698 + Tool usage (all time) (usegalaxy.org): 998 + Tool usage (all time) (usegalaxy.org.au): 77 + Tool usage (all time) - all main servers: 1773 + ToolShed categories: + - Fasta Manipulation + - Statistics + - RNA + - Micro-array Analysis + ToolShed id: length_and_gc_content + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-limma + Conda version: 3.58.1 + Date of first commit of the suite: '2019-02-17' + Description: Perform RNA-Seq differential expression analysis using limma voom pipeline + EDAM operation: + - RNA-Seq analysis + EDAM operation (no superclasses): + - RNA-Seq analysis + EDAM topic: + - Molecular biology + - Genetics + EDAM topic (no superclasses): + - Molecular biology + - Genetics + Galaxy tool ids: + - limma_voom + Galaxy wrapper id: limma_voom + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom + Galaxy wrapper version: 3.58.1 + No. of tool users (5 years) (usegalaxy.eu): 23442 + No. of tool users (5 years) (usegalaxy.org): 45734 + No. of tool users (5 years) (usegalaxy.org.au): 9327 + No. of tool users (5 years) - all main servers: 78503 + No. of tool users (all time) (usegalaxy.eu): 24466 + No. of tool users (all time) (usegalaxy.org): 49342 + No. of tool users (all time) (usegalaxy.org.au): 9517 + No. of tool users (all time) - all main servers: 83325 + Source: http://bioconductor.org/packages/release/bioc/html/limma.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2379 + Tool usage (5 years) (usegalaxy.org): 4565 + Tool usage (5 years) (usegalaxy.org.au): 835 + Tool usage (5 years) - all main servers: 7779 + Tool usage (all time) (usegalaxy.eu): 2475 + Tool usage (all time) (usegalaxy.org): 5032 + Tool usage (all time) (usegalaxy.org.au): 842 + Tool usage (all time) - all main servers: 8349 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: limma_voom + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Data analysis, linear models and differential expression for + microarray data. + bio.tool id: limma + bio.tool ids: + - limma + bio.tool name: limma +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2023-07-05' + Description: Identification of SARS-CoV-2 related metagenomic mutations based on + a single (or a list of) variant(s) file(s) + EDAM operation: + - Variant calling + EDAM operation (no superclasses): + - Variant calling + EDAM topic: + - Metagenomics + - Gene transcripts + - Evolutionary biology + - Sequencing + - Genetic variation + EDAM topic (no superclasses): + - Metagenomics + - Gene transcripts + - Evolutionary biology + - Sequencing + - Genetic variation + Galaxy tool ids: + - lineagespot + Galaxy wrapper id: lineagespot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot + Galaxy wrapper version: 1.6.0 + No. of tool users (5 years) (usegalaxy.eu): 39 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 39 + No. of tool users (all time) (usegalaxy.eu): 39 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 39 + Source: https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Metagenomics + - Sequence Analysis + ToolShed id: lineagespot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Lineagespot is a framework written in R, and aims to identify + and assign different SARS-CoV-2 lineages based on a single variant file (i.e., + variant calling format). + bio.tool id: lineagespot + bio.tool ids: + - lineagespot + bio.tool name: lineagespot +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: links + Conda version: 2.0.1 + Date of first commit of the suite: '2022-02-23' + Description: Scaffold genome assemblies with long reads. + EDAM operation: + - Scaffolding + - Genome assembly + - Read mapping + - Read pre-processing + - Sequence trimming + EDAM operation (no superclasses): + - Scaffolding + - Genome assembly + - Read mapping + - Read pre-processing + - Sequence trimming + EDAM topic: + - Sequence assembly + - Mapping + - Sequencing + EDAM topic (no superclasses): + - Sequence assembly + - Mapping + - Sequencing + Galaxy tool ids: + - links + Galaxy wrapper id: links + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/links + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/links + Galaxy wrapper version: 2.0.1 + No. of tool users (5 years) (usegalaxy.eu): 512 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 480 + No. of tool users (5 years) - all main servers: 992 + No. of tool users (all time) (usegalaxy.eu): 512 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 480 + No. of tool users (all time) - all main servers: 992 + Source: https://github.com/bcgsc/LINKS + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 126 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 65 + Tool usage (5 years) - all main servers: 191 + Tool usage (all time) (usegalaxy.eu): 126 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 65 + Tool usage (all time) - all main servers: 191 + ToolShed categories: + - Assembly + ToolShed id: links + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics + application for scaffolding genome assemblies with long reads, such as those produced + by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft + genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other + draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. + bio.tool id: links + bio.tool ids: + - links + bio.tool name: LINKS +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: lofreq + Conda version: 2.1.5 + Date of first commit of the suite: '2019-12-17' + Description: LoFreq is a fast and sensitive variant-caller for inferring SNVs and + indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand + other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment + uncertainty), which are usually ignored by other methods or onlyused for filtering. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - lofreq_alnqual + - lofreq_call + - lofreq_filter + - lofreq_indelqual + - lofreq_viterbi + Galaxy wrapper id: lofreq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq + Galaxy wrapper version: 2.1.5 + No. of tool users (5 years) (usegalaxy.eu): 4176367 + No. of tool users (5 years) (usegalaxy.org): 509615 + No. of tool users (5 years) (usegalaxy.org.au): 106342 + No. of tool users (5 years) - all main servers: 4792324 + No. of tool users (all time) (usegalaxy.eu): 4176367 + No. of tool users (all time) (usegalaxy.org): 509615 + No. of tool users (all time) (usegalaxy.org.au): 106342 + No. of tool users (all time) - all main servers: 4792324 + Source: https://csb5.github.io/lofreq/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4301 + Tool usage (5 years) (usegalaxy.org): 8213 + Tool usage (5 years) (usegalaxy.org.au): 1815 + Tool usage (5 years) - all main servers: 14329 + Tool usage (all time) (usegalaxy.eu): 4301 + Tool usage (all time) (usegalaxy.org): 8213 + Tool usage (all time) (usegalaxy.org.au): 1815 + Tool usage (all time) - all main servers: 14329 + ToolShed categories: + - Variant Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 4 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 4 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 4 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: lorikeet + Conda version: '20' + Date of first commit of the suite: '2018-05-07' + Description: Tools for M. tuberculosis DNA fingerprinting (spoligotyping) + EDAM operation: + - Sequence analysis + - Genotyping + EDAM operation (no superclasses): + - Sequence analysis + - Genotyping + EDAM topic: + - Genotype and phenotype + EDAM topic (no superclasses): + - Genotype and phenotype + Galaxy tool ids: + - lorikeet_spoligotype + Galaxy wrapper id: lorikeet + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet + Galaxy wrapper source: https://github.com/AbeelLab/lorikeet + Galaxy wrapper version: '20' + No. of tool users (5 years) (usegalaxy.eu): 822 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 822 + No. of tool users (all time) (usegalaxy.eu): 822 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 822 + Source: https://github.com/AbeelLab/lorikeet + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 14 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 14 + Tool usage (all time) (usegalaxy.eu): 14 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 14 + ToolShed categories: + - Sequence Analysis + ToolShed id: lorikeet_spoligotype + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Tools for M. tuberculosis DNA fingerprinting (spoligotyping) + bio.tool id: lorikeet + bio.tool ids: + - lorikeet + bio.tool name: lorikeet +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: lumpy-sv + Conda version: 0.3.1 + Date of first commit of the suite: '2020-11-12' + Description: LUMPY - a general probabilistic framework for structural variant discovery + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - lumpy_prep + - lumpy_sv + Galaxy wrapper id: lumpy_sv + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv + Galaxy wrapper source: https://github.com/arq5x/lumpy-sv + Galaxy wrapper version: 0.3.1 + No. of tool users (5 years) (usegalaxy.eu): 1534 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1534 + No. of tool users (all time) (usegalaxy.eu): 1534 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1534 + Source: http://layerlab.org/software/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 199 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 199 + Tool usage (all time) (usegalaxy.eu): 199 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 199 + ToolShed categories: + - Variant Analysis + ToolShed id: lumpy_sv + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: m6anet + Conda version: 2.1.0 + Date of first commit of the suite: '2023-10-25' + Description: m6anet to detect m6A RNA modifications from nanopore data + EDAM operation: + - Quantification + - Imputation + - Gene expression profiling + EDAM operation (no superclasses): + - Quantification + - Imputation + - Gene expression profiling + EDAM topic: + - RNA-Seq + - Transcriptomics + - RNA + - Machine learning + EDAM topic (no superclasses): + - RNA-Seq + - Transcriptomics + - RNA + - Machine learning + Galaxy tool ids: + - m6anet + Galaxy wrapper id: m6anet + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet + Galaxy wrapper version: 2.1.0 + No. of tool users (5 years) (usegalaxy.eu): 44 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 44 + No. of tool users (all time) (usegalaxy.eu): 44 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 44 + Source: https://m6anet.readthedocs.io/en/latest + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Sequence Analysis + ToolShed id: m6anet + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Detection of m6A from direct RNA sequencing using a Multiple + Instance Learning framework. + bio.tool id: m6Anet + bio.tool ids: + - m6Anet + bio.tool name: m6Anet +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-maaslin2 + Conda version: 1.18.0 + Date of first commit of the suite: '2021-11-05' + Description: MaAsLin2 is comprehensive R package for efficiently determining multivariable + association between microbial meta'omic features and clinical metadata. + EDAM operation: + - Filtering + - Statistical calculation + - Standardisation and normalisation + - Visualisation + EDAM operation (no superclasses): + - Filtering + - Standardisation and normalisation + - Visualisation + EDAM topic: + - Metagenomics + - Statistics and probability + EDAM topic (no superclasses): + - Metagenomics + - Statistics and probability + Galaxy tool ids: + - maaslin2 + Galaxy wrapper id: maaslin2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 + Galaxy wrapper source: https://github.com/biobakery/Maaslin2 + Galaxy wrapper version: 1.18.0 + No. of tool users (5 years) (usegalaxy.eu): 2835 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2835 + No. of tool users (all time) (usegalaxy.eu): 2835 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2835 + Source: http://huttenhower.sph.harvard.edu/maaslin + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 59 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 59 + Tool usage (all time) (usegalaxy.eu): 59 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 59 + ToolShed categories: + - Metagenomics + ToolShed id: maaslin2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: "MaAsLin2 is comprehensive R package for efficiently determining\ + \ multivariable association between phenotypes, environments, exposures, covariates\ + \ and microbial meta\u2019omic features. MaAsLin2 relies on general linear models\ + \ to accommodate most modern epidemiological study designs, including cross-sectional\ + \ and longitudinal, and offers a variety of data exploration, normalization, and\ + \ transformation methods." + bio.tool id: maaslin2 + bio.tool ids: + - maaslin2 + bio.tool name: MaAsLin2 +- Available on UseGalaxy.eu: 9 + Available on UseGalaxy.fr: 9 + Available on UseGalaxy.org (Main): 9 + Available on UseGalaxy.org.au: 9 + Conda id: macs2 + Conda version: 2.2.9.1 + Date of first commit of the suite: '2018-01-21' + Description: MACS - Model-based Analysis of ChIP-Seq + EDAM operation: + - Peak calling + - Enrichment analysis + - Gene regulatory network analysis + EDAM operation (no superclasses): + - Peak calling + - Enrichment analysis + - Gene regulatory network analysis + EDAM topic: + - ChIP-seq + - Molecular interactions, pathways and networks + - Transcription factors and regulatory sites + EDAM topic (no superclasses): + - ChIP-seq + - Molecular interactions, pathways and networks + - Transcription factors and regulatory sites + Galaxy tool ids: + - macs2_bdgbroadcall + - macs2_bdgcmp + - macs2_bdgdiff + - macs2_bdgpeakcall + - macs2_callpeak + - macs2_filterdup + - macs2_predictd + - macs2_randsample + - macs2_refinepeak + Galaxy wrapper id: macs2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 + Galaxy wrapper version: 2.2.9.1 + No. of tool users (5 years) (usegalaxy.eu): 87810 + No. of tool users (5 years) (usegalaxy.org): 153500 + No. of tool users (5 years) (usegalaxy.org.au): 10988 + No. of tool users (5 years) - all main servers: 252298 + No. of tool users (all time) (usegalaxy.eu): 96069 + No. of tool users (all time) (usegalaxy.org): 227569 + No. of tool users (all time) (usegalaxy.org.au): 12301 + No. of tool users (all time) - all main servers: 335939 + Source: https://github.com/taoliu/MACS + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4980 + Tool usage (5 years) (usegalaxy.org): 12946 + Tool usage (5 years) (usegalaxy.org.au): 692 + Tool usage (5 years) - all main servers: 18618 + Tool usage (all time) (usegalaxy.eu): 5629 + Tool usage (all time) (usegalaxy.org): 18825 + Tool usage (all time) (usegalaxy.org.au): 807 + Tool usage (all time) - all main servers: 25261 + ToolShed categories: + - Sequence Analysis + - Statistics + ToolShed id: macs2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 9 + Tools available on Galaxy@Pasteur: 9 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 9 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 9 + Tools available on UseGalaxy.cz: 9 + Tools available on UseGalaxy.eu: 9 + Tools available on UseGalaxy.fr: 9 + Tools available on UseGalaxy.no: 9 + Tools available on UseGalaxy.org (Main): 9 + Tools available on UseGalaxy.org.au: 9 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 9 + UseGalaxy.cz: 9 + UseGalaxy.eu: 9 + UseGalaxy.fr: 9 + UseGalaxy.no: 9 + UseGalaxy.or: 9 + biii: null + bio.tool description: Model-based Analysis of ChIP-seq data. + bio.tool id: macs + bio.tool ids: + - macs + bio.tool name: MACS +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-08-12' + Description: MAF Coverage statistics + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - maf_stats1 + Galaxy wrapper id: maf_stats + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ + Galaxy wrapper version: 1.0.2+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 15 + No. of tool users (5 years) (usegalaxy.org): 227 + No. of tool users (5 years) (usegalaxy.org.au): 1 + No. of tool users (5 years) - all main servers: 243 + No. of tool users (all time) (usegalaxy.eu): 21 + No. of tool users (all time) (usegalaxy.org): 2470 + No. of tool users (all time) (usegalaxy.org.au): 1 + No. of tool users (all time) - all main servers: 2492 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 52 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 60 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 464 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 474 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: maf_stats + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 1 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 1 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 1 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 5 + Conda id: mageck + Conda version: 0.5.9.5 + Date of first commit of the suite: '2018-03-25' + Description: Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is + a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 + knockout screens technology. + EDAM operation: + - Genetic variation analysis + EDAM operation (no superclasses): + - Genetic variation analysis + EDAM topic: + - Genetics + - Genetic variation + - Genomics + EDAM topic (no superclasses): + - Genetics + - Genetic variation + - Genomics + Galaxy tool ids: + - mageck_count + - mageck_gsea + - mageck_mle + - mageck_pathway + - mageck_test + Galaxy wrapper id: mageck + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck + Galaxy wrapper version: 0.5.9.2 + No. of tool users (5 years) (usegalaxy.eu): 11761 + No. of tool users (5 years) (usegalaxy.org): 5762 + No. of tool users (5 years) (usegalaxy.org.au): 5610 + No. of tool users (5 years) - all main servers: 23133 + No. of tool users (all time) (usegalaxy.eu): 12093 + No. of tool users (all time) (usegalaxy.org): 5762 + No. of tool users (all time) (usegalaxy.org.au): 5610 + No. of tool users (all time) - all main servers: 23465 + Source: https://sourceforge.net/projects/mageck/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 873 + Tool usage (5 years) (usegalaxy.org): 473 + Tool usage (5 years) (usegalaxy.org.au): 343 + Tool usage (5 years) - all main servers: 1689 + Tool usage (all time) (usegalaxy.eu): 889 + Tool usage (all time) (usegalaxy.org): 473 + Tool usage (all time) (usegalaxy.org.au): 343 + Tool usage (all time) - all main servers: 1705 + ToolShed categories: + - Genome editing + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 5 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: Computational tool to identify important genes from the recent + genome-scale CRISPR-Cas9 knockout screens technology. + bio.tool id: mageck + bio.tool ids: + - mageck + bio.tool name: MAGeCK +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: maker + Conda version: 3.01.03 + Date of first commit of the suite: '2017-10-13' + Description: MAKER is a portable and easily configurable genome annotation pipeline.Its + purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently + annotate their genomes and to create genome databases. + EDAM operation: + - Genome annotation + EDAM operation (no superclasses): + - Genome annotation + EDAM topic: + - Genomics + - DNA + - Sequence analysis + EDAM topic (no superclasses): + - Genomics + - DNA + - Sequence analysis + Galaxy tool ids: + - maker + - maker_map_ids + Galaxy wrapper id: maker + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker + Galaxy wrapper version: 2.31.11 + No. of tool users (5 years) (usegalaxy.eu): 6417 + No. of tool users (5 years) (usegalaxy.org): 7235 + No. of tool users (5 years) (usegalaxy.org.au): 4112 + No. of tool users (5 years) - all main servers: 17764 + No. of tool users (all time) (usegalaxy.eu): 6861 + No. of tool users (all time) (usegalaxy.org): 7235 + No. of tool users (all time) (usegalaxy.org.au): 4112 + No. of tool users (all time) - all main servers: 18208 + Source: http://www.yandell-lab.org/software/maker.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1315 + Tool usage (5 years) (usegalaxy.org): 1858 + Tool usage (5 years) (usegalaxy.org.au): 902 + Tool usage (5 years) - all main servers: 4075 + Tool usage (all time) (usegalaxy.eu): 1366 + Tool usage (all time) (usegalaxy.org): 1858 + Tool usage (all time) (usegalaxy.org.au): 902 + Tool usage (all time) - all main servers: 4126 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: "Portable and easily configurable genome annotation pipeline.\ + \ It\u2019s purpose is to allow smaller eukaryotic and prokaryotic genome projects\ + \ to independently annotate their genomes and to create genome databases." + bio.tool id: maker + bio.tool ids: + - maker + bio.tool name: MAKER +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: malt + Conda version: '0.62' + Date of first commit of the suite: '2021-11-12' + Description: Aligns an input sequence (DNA or proteins) against an index representing + a collection of reference DNA or protein sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - malt_run + Galaxy wrapper id: malt + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt + Galaxy wrapper version: 0.5.3 + No. of tool users (5 years) (usegalaxy.eu): 24 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 24 + No. of tool users (all time) (usegalaxy.eu): 24 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 24 + Source: https://github.com/husonlab/malt + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Next Gen Mappers + ToolShed id: malt_run + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-10-13' + Description: Map a parameter value to another value + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - map_param_value + Galaxy wrapper id: map_param_value + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 3780 + No. of tool users (5 years) (usegalaxy.org): 1012 + No. of tool users (5 years) (usegalaxy.org.au): 105 + No. of tool users (5 years) - all main servers: 4897 + No. of tool users (all time) (usegalaxy.eu): 3780 + No. of tool users (all time) (usegalaxy.org): 1012 + No. of tool users (all time) (usegalaxy.org.au): 105 + No. of tool users (all time) - all main servers: 4897 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 67 + Tool usage (5 years) (usegalaxy.org): 57 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 127 + Tool usage (all time) (usegalaxy.eu): 67 + Tool usage (all time) (usegalaxy.org): 57 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 127 + ToolShed categories: + - Text Manipulation + ToolShed id: map_param_value + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl + Conda version: null + Date of first commit of the suite: '2023-08-02' + Description: fast and accurate sequence read classification tool designed to assign + taxonomy and OTU classifications to ribosomal RNA sequences. + EDAM operation: + - k-mer counting + EDAM operation (no superclasses): + - k-mer counting + EDAM topic: + - Functional, regulatory and non-coding RNA + - Sequence analysis + - Sequence sites, features and motifs + EDAM topic (no superclasses): + - Functional, regulatory and non-coding RNA + - Sequence analysis + - Sequence sites, features and motifs + Galaxy tool ids: + - mapseq + Galaxy wrapper id: mapseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq + Galaxy wrapper version: 2.1.1b + No. of tool users (5 years) (usegalaxy.eu): 7871 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7871 + No. of tool users (all time) (usegalaxy.eu): 7871 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7871 + Source: https://github.com/jfmrod/MAPseq + Status: To update + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 32 + Tool usage (all time) (usegalaxy.eu): 32 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 32 + ToolShed categories: + - Metagenomics + ToolShed id: mapseq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Highly efficient k-mer search with confidence estimates, for + rRNA sequence analysis . + bio.tool id: mapseq + bio.tool ids: + - mapseq + bio.tool name: MAPseq +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: mash + Conda version: '2.3' + Date of first commit of the suite: '2019-01-23' + Description: Fast genome and metagenome distance estimation using MinHash + EDAM operation: + - Sequence distance matrix generation + EDAM operation (no superclasses): + - Sequence distance matrix generation + EDAM topic: + - Genomics + - Metagenomics + - Statistics and probability + - Sequence analysis + - DNA mutation + EDAM topic (no superclasses): + - Metagenomics + - Statistics and probability + - Sequence analysis + - DNA mutation + Galaxy tool ids: + - mash_screen + - mash_sketch + Galaxy wrapper id: mash + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash + Galaxy wrapper version: '2.3' + No. of tool users (5 years) (usegalaxy.eu): 10119 + No. of tool users (5 years) (usegalaxy.org): 19 + No. of tool users (5 years) (usegalaxy.org.au): 647 + No. of tool users (5 years) - all main servers: 10785 + No. of tool users (all time) (usegalaxy.eu): 10119 + No. of tool users (all time) (usegalaxy.org): 19 + No. of tool users (all time) (usegalaxy.org.au): 647 + No. of tool users (all time) - all main servers: 10785 + Source: https://github.com/marbl/Mash + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 61 + Tool usage (5 years) (usegalaxy.org): 9 + Tool usage (5 years) (usegalaxy.org.au): 7 + Tool usage (5 years) - all main servers: 77 + Tool usage (all time) (usegalaxy.eu): 61 + Tool usage (all time) (usegalaxy.org): 9 + Tool usage (all time) (usegalaxy.org.au): 7 + Tool usage (all time) - all main servers: 77 + ToolShed categories: + - Metagenomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Fast genome and metagenome distance estimation using MinHash. + bio.tool id: mash + bio.tool ids: + - mash + bio.tool name: Mash +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: mashmap + Conda version: 3.1.3 + Date of first commit of the suite: '2024-02-26' + Description: Fast local alignment boundaries + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mashmap + Galaxy wrapper id: mashmap + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap + Galaxy wrapper version: 3.1.3 + No. of tool users (5 years) (usegalaxy.eu): 894 + No. of tool users (5 years) (usegalaxy.org): 81 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 975 + No. of tool users (all time) (usegalaxy.eu): 894 + No. of tool users (all time) (usegalaxy.org): 81 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 975 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 12 + Tool usage (5 years) (usegalaxy.org): 5 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 5 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 17 + ToolShed categories: + - Sequence Analysis + ToolShed id: mashmap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: coreutils + Conda version: '8.25' + Date of first commit of the suite: '2017-05-09' + Description: Identify significantly differential expression profiles in time-course + microarray experiments + EDAM operation: + - Regression analysis + EDAM operation (no superclasses): + - Regression analysis + EDAM topic: + - Gene expression + - Molecular genetics + - Microarray experiment + - RNA-Seq + EDAM topic (no superclasses): + - Gene expression + - Microarray experiment + - RNA-Seq + Galaxy tool ids: + - masigpro + Galaxy wrapper id: masigpro + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro + Galaxy wrapper version: 1.49.3 + No. of tool users (5 years) (usegalaxy.eu): 471 + No. of tool users (5 years) (usegalaxy.org): 589 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1060 + No. of tool users (all time) (usegalaxy.eu): 582 + No. of tool users (all time) (usegalaxy.org): 589 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1171 + Source: https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 35 + Tool usage (5 years) (usegalaxy.org): 80 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 115 + Tool usage (all time) (usegalaxy.eu): 40 + Tool usage (all time) (usegalaxy.org): 80 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 120 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: masigpro + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Regression based approach to find genes for which there are + significant gene expression profile differences between experimental groups in + time course microarray and RNA-Seq experiments. + bio.tool id: masigpro + bio.tool ids: + - masigpro + bio.tool name: maSigPro +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: maxbin2 + Conda version: 2.2.7 + Date of first commit of the suite: '2019-10-24' + Description: clusters metagenomic contigs into bins + EDAM operation: + - Sequence assembly + EDAM operation (no superclasses): + - Sequence assembly + EDAM topic: + - Metagenomics + - Sequence assembly + - Microbiology + EDAM topic (no superclasses): + - Metagenomics + - Sequence assembly + - Microbiology + Galaxy tool ids: + - maxbin2 + Galaxy wrapper id: maxbin2 + Galaxy wrapper owner: mbernt + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 2798 + No. of tool users (5 years) (usegalaxy.org): 2452 + No. of tool users (5 years) (usegalaxy.org.au): 914 + No. of tool users (5 years) - all main servers: 6164 + No. of tool users (all time) (usegalaxy.eu): 2798 + No. of tool users (all time) (usegalaxy.org): 2452 + No. of tool users (all time) (usegalaxy.org.au): 914 + No. of tool users (all time) - all main servers: 6164 + Source: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 314 + Tool usage (5 years) (usegalaxy.org): 508 + Tool usage (5 years) (usegalaxy.org.au): 89 + Tool usage (5 years) - all main servers: 911 + Tool usage (all time) (usegalaxy.eu): 314 + Tool usage (all time) (usegalaxy.org): 508 + Tool usage (all time) (usegalaxy.org.au): 89 + Tool usage (all time) - all main servers: 911 + ToolShed categories: + - Metagenomics + ToolShed id: maxbin2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Software for binning assembled metagenomic sequences based + on an Expectation-Maximization algorithm. + bio.tool id: maxbin + bio.tool ids: + - maxbin + bio.tool name: MaxBin +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mcl + Conda version: '22.282' + Date of first commit of the suite: '2022-05-12' + Description: The Markov Cluster Algorithm, a cluster algorithm for graphs + EDAM operation: + - Clustering + - Network analysis + - Gene regulatory network analysis + EDAM operation (no superclasses): + - Clustering + - Gene regulatory network analysis + EDAM topic: + - Molecular interactions, pathways and networks + EDAM topic (no superclasses): + - Molecular interactions, pathways and networks + Galaxy tool ids: + - mcl + Galaxy wrapper id: mcl + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/mcl + Galaxy wrapper version: '22.282' + No. of tool users (5 years) (usegalaxy.eu): 35 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 35 + No. of tool users (all time) (usegalaxy.eu): 35 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 35 + Source: https://micans.org/mcl/man/mcl.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 13 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 13 + Tool usage (all time) (usegalaxy.eu): 13 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 13 + ToolShed categories: + - Sequence Analysis + ToolShed id: mcl + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: MCL is a clustering algorithm widely used in bioinformatics + and gaining traction in other fields. + bio.tool id: mcl + bio.tool ids: + - mcl + bio.tool name: MCL +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: medaka + Conda version: 2.0.1 + Date of first commit of the suite: '2020-08-24' + Description: Sequence correction provided by ONT Research + EDAM operation: + - Base-calling + - Variant calling + - Sequence assembly + EDAM operation (no superclasses): + - Base-calling + - Variant calling + - Sequence assembly + EDAM topic: + - Sequence assembly + - Machine learning + EDAM topic (no superclasses): + - Sequence assembly + - Machine learning + Galaxy tool ids: + - medaka_consensus + - medaka_consensus_pipeline + - medaka_snp + - medaka_variant + Galaxy wrapper id: medaka + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka + Galaxy wrapper version: 1.7.2 + No. of tool users (5 years) (usegalaxy.eu): 117975 + No. of tool users (5 years) (usegalaxy.org): 55063 + No. of tool users (5 years) (usegalaxy.org.au): 9325 + No. of tool users (5 years) - all main servers: 182363 + No. of tool users (all time) (usegalaxy.eu): 117975 + No. of tool users (all time) (usegalaxy.org): 55063 + No. of tool users (all time) (usegalaxy.org.au): 9325 + No. of tool users (all time) - all main servers: 182363 + Source: https://github.com/nanoporetech/medaka + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1693 + Tool usage (5 years) (usegalaxy.org): 796 + Tool usage (5 years) (usegalaxy.org.au): 639 + Tool usage (5 years) - all main servers: 3128 + Tool usage (all time) (usegalaxy.eu): 1693 + Tool usage (all time) (usegalaxy.org): 796 + Tool usage (all time) (usegalaxy.org.au): 639 + Tool usage (all time) - all main servers: 3128 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 2 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: medaka is a tool to create consensus sequences and variant + calls from nanopore sequencing data. This task is performed using neural networks + applied a pileup of individual sequencing reads against a draft assembly. + bio.tool id: medaka + bio.tool ids: + - medaka + bio.tool name: Medaka +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: megahit + Conda version: 1.2.9 + Date of first commit of the suite: '2017-09-22' + Description: An ultra-fast single-node solution for large and complex metagenomics + assembly via succinct de Bruijn graph. + EDAM operation: + - Genome assembly + EDAM operation (no superclasses): + - Genome assembly + EDAM topic: + - Metagenomics + - Sequencing + - Ecology + - Sequence assembly + EDAM topic (no superclasses): + - Metagenomics + - Sequencing + - Sequence assembly + Galaxy tool ids: + - megahit + Galaxy wrapper id: megahit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit + Galaxy wrapper version: 1.2.9 + No. of tool users (5 years) (usegalaxy.eu): 12692 + No. of tool users (5 years) (usegalaxy.org): 16645 + No. of tool users (5 years) (usegalaxy.org.au): 6214 + No. of tool users (5 years) - all main servers: 35551 + No. of tool users (all time) (usegalaxy.eu): 13292 + No. of tool users (all time) (usegalaxy.org): 16645 + No. of tool users (all time) (usegalaxy.org.au): 6214 + No. of tool users (all time) - all main servers: 36151 + Source: https://github.com/voutcn/megahit + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1349 + Tool usage (5 years) (usegalaxy.org): 2140 + Tool usage (5 years) (usegalaxy.org.au): 431 + Tool usage (5 years) - all main servers: 3920 + Tool usage (all time) (usegalaxy.eu): 1400 + Tool usage (all time) (usegalaxy.org): 2140 + Tool usage (all time) (usegalaxy.org.au): 431 + Tool usage (all time) - all main servers: 3971 + ToolShed categories: + - Sequence Analysis + - Assembly + - Metagenomics + ToolShed id: megahit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Single node assembler for large and complex metagenomics NGS + reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory + usage, whereas its goal is not to make memory usage as low as possible. + bio.tool id: megahit + bio.tool ids: + - megahit + bio.tool name: MEGAHIT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: megahit + Conda version: 1.2.9 + Date of first commit of the suite: '2018-11-09' + Description: A subprogram within the Megahit toolkit for converting contigs to assembly + graphs (fastg) + EDAM operation: + - Genome assembly + EDAM operation (no superclasses): + - Genome assembly + EDAM topic: + - Metagenomics + - Sequencing + - Ecology + - Sequence assembly + EDAM topic (no superclasses): + - Metagenomics + - Sequencing + - Sequence assembly + Galaxy tool ids: + - megahit_contig2fastg + Galaxy wrapper id: megahit_contig2fastg + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg + Galaxy wrapper version: 1.1.3 + No. of tool users (5 years) (usegalaxy.eu): 513 + No. of tool users (5 years) (usegalaxy.org): 74 + No. of tool users (5 years) (usegalaxy.org.au): 10 + No. of tool users (5 years) - all main servers: 597 + No. of tool users (all time) (usegalaxy.eu): 557 + No. of tool users (all time) (usegalaxy.org): 74 + No. of tool users (all time) (usegalaxy.org.au): 10 + No. of tool users (all time) - all main servers: 641 + Source: https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp + Status: To update + Tool usage (5 years) (usegalaxy.eu): 152 + Tool usage (5 years) (usegalaxy.org): 35 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 191 + Tool usage (all time) (usegalaxy.eu): 155 + Tool usage (all time) (usegalaxy.org): 35 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 194 + ToolShed categories: + - Sequence Analysis + - Assembly + - Metagenomics + ToolShed id: megahit_contig2fastg + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Single node assembler for large and complex metagenomics NGS + reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory + usage, whereas its goal is not to make memory usage as low as possible. + bio.tool id: megahit + bio.tool ids: + - megahit + bio.tool name: MEGAHIT +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: megan + Conda version: 6.25.9 + Date of first commit of the suite: '2021-11-24' + Description: MEGAN Community Edition - Interactive exploration and analysis of large-scale + microbiome sequencing data. MEGAN is a tool for studying the taxonomic content + of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing + step, a sequence alignment of all reads against a suitable database of reference + DNA or proteinsequences must be performed to produce an input file for the program. + MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome + data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile + that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). + EDAM operation: + - Sequence analysis + - Taxonomic classification + EDAM operation (no superclasses): + - Sequence analysis + - Taxonomic classification + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - megan_blast2lca + - megan_blast2rma + - megan_daa2info + - megan_daa2rma + - megan_daa_meganizer + - megan_read_extractor + - megan_sam2rma + Galaxy wrapper id: megan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan + Galaxy wrapper version: 6.21.7 + No. of tool users (5 years) (usegalaxy.eu): 4130 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4130 + No. of tool users (all time) (usegalaxy.eu): 4130 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4130 + Source: https://github.com/husonlab/megan-ce + Status: To update + Tool usage (5 years) (usegalaxy.eu): 447 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 447 + Tool usage (all time) (usegalaxy.eu): 447 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 447 + ToolShed categories: + - Sequence Analysis + ToolShed id: megan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + biii: null + bio.tool description: "Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer\x9D\ + ) is a new computer program that allows laptop analysis of large metagenomic datasets.\ + \ In a preprocessing step, the set of DNA reads (or contigs) is compared against\ + \ databases of known sequences using BLAST or another comparison tool. MEGAN can\ + \ then be used to compute and interactively explore the taxonomical content of\ + \ the dataset, employing the NCBI taxonomy to summarize and order the results." + bio.tool id: megan + bio.tool ids: + - megan + bio.tool name: MEGAN +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 0 + Conda id: meme + Conda version: 5.5.7 + Date of first commit of the suite: '2018-04-25' + Description: The MEME Suite allows the biologist to discover novel motifs in collections + of unaligned nucleotideor protein sequences, and to perform a wide variety of + other motif-based analyses. + EDAM operation: + - Nucleic acid feature detection + - Protein feature detection + - Statistical calculation + EDAM operation (no superclasses): + - Nucleic acid feature detection + - Protein feature detection + - Statistical calculation + EDAM topic: + - Data mining + - Sequence analysis + - Genetic variation + - Statistics and probability + EDAM topic (no superclasses): + - Data mining + - Sequence analysis + - Genetic variation + - Statistics and probability + Galaxy tool ids: + - meme_dreme + - meme_fimo + - meme_meme + - meme_psp_gen + Galaxy wrapper id: meme + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme + Galaxy wrapper version: 5.5.6 + No. of tool users (5 years) (usegalaxy.eu): 20990 + No. of tool users (5 years) (usegalaxy.org): 10975 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 31965 + No. of tool users (all time) (usegalaxy.eu): 22979 + No. of tool users (all time) (usegalaxy.org): 25929 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 48908 + Source: http://meme-suite.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 762 + Tool usage (5 years) (usegalaxy.org): 1551 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2313 + Tool usage (all time) (usegalaxy.eu): 892 + Tool usage (all time) (usegalaxy.org): 3249 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4141 + ToolShed categories: + - ChIP-seq + ToolShed id: meme + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 4 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 4 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 2 + UseGalaxy.no: 4 + UseGalaxy.or: 3 + biii: null + bio.tool description: An algorithm that discovers one or more motifs in a collection + of DNA or protein sequences by using the technique of expectation maximization + to fit a two-component finite mixture model to the set of sequences. + bio.tool id: meme_meme + bio.tool ids: + - meme_fimo + - meme_meme + bio.tool name: meme_meme +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: graphicsmagick + Conda version: 1.3.26 + Date of first commit of the suite: '2018-03-15' + Description: Performs motif discovery, motif enrichment analysis and clustering + on large nucleotide datasets. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - meme_chip + Galaxy wrapper id: meme_chip + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip + Galaxy wrapper version: 4.11.2 + No. of tool users (5 years) (usegalaxy.eu): 6413 + No. of tool users (5 years) (usegalaxy.org): 7260 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 13673 + No. of tool users (all time) (usegalaxy.eu): 7000 + No. of tool users (all time) (usegalaxy.org): 7260 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 14260 + Source: http://meme-suite.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 705 + Tool usage (5 years) (usegalaxy.org): 1171 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1876 + Tool usage (all time) (usegalaxy.eu): 743 + Tool usage (all time) (usegalaxy.org): 1171 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1914 + ToolShed categories: + - ChIP-seq + ToolShed id: meme_chip + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: meningotype + Conda version: 0.8.5 + Date of first commit of the suite: '2023-06-06' + Description: Assign sequence type to N. meningitidis genome assemblies + EDAM operation: + - Genotyping + - Multilocus sequence typing + EDAM operation (no superclasses): + - Multilocus sequence typing + EDAM topic: + - Microbiology + - Genotype and phenotype + EDAM topic (no superclasses): + - Microbiology + - Genotype and phenotype + Galaxy tool ids: + - meningotype + Galaxy wrapper id: meningotype + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype + Galaxy wrapper version: 0.8.5 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/MDU-PHL/meningotype + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: meningotype + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: In silico typing of Neisseria meningitidis contigs. + bio.tool id: meningotype + bio.tool ids: + - meningotype + bio.tool name: meningotype +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: merlin + Conda version: 1.1.2 + Date of first commit of the suite: '2020-04-15' + Description: Pedigree Analysis package + EDAM operation: + - Haplotype mapping + - Genetic mapping + EDAM operation (no superclasses): + - Haplotype mapping + EDAM topic: + - GWAS study + - Mapping + EDAM topic (no superclasses): + - GWAS study + - Mapping + Galaxy tool ids: + - merlin + Galaxy wrapper id: merlin + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ + Galaxy wrapper version: 1.1.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://csg.sph.umich.edu/abecasis/Merlin/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: merlin + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: Can be used for parametric and non-parametric linkage analysis, + regression-based linkage analysis or association analysis for quantitative traits, + ibd and kinship estimation, haplotyping, error detection and simulation + bio.tool id: merlin + bio.tool ids: + - merlin + bio.tool name: Merlin +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: merqury + Conda version: '1.3' + Date of first commit of the suite: '2021-04-18' + Description: Merqury is a tool for evaluating genomes assemblies based of k-mer + operations. + EDAM operation: + - Genome assembly + - k-mer counting + - Scaffolding + - Phasing + - De-novo assembly + EDAM operation (no superclasses): + - Genome assembly + - k-mer counting + - Scaffolding + - Phasing + - De-novo assembly + EDAM topic: + - Sequence assembly + - Whole genome sequencing + - Plant biology + EDAM topic (no superclasses): + - Sequence assembly + - Whole genome sequencing + - Plant biology + Galaxy tool ids: + - merqury + - merquryplot + Galaxy wrapper id: merqury + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury + Galaxy wrapper version: '1.3' + No. of tool users (5 years) (usegalaxy.eu): 3150 + No. of tool users (5 years) (usegalaxy.org): 730 + No. of tool users (5 years) (usegalaxy.org.au): 1183 + No. of tool users (5 years) - all main servers: 5063 + No. of tool users (all time) (usegalaxy.eu): 3150 + No. of tool users (all time) (usegalaxy.org): 730 + No. of tool users (all time) (usegalaxy.org.au): 1183 + No. of tool users (all time) - all main servers: 5063 + Source: https://github.com/marbl/merqury + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 477 + Tool usage (5 years) (usegalaxy.org): 196 + Tool usage (5 years) (usegalaxy.org.au): 151 + Tool usage (5 years) - all main servers: 824 + Tool usage (all time) (usegalaxy.eu): 477 + Tool usage (all time) (usegalaxy.org): 196 + Tool usage (all time) (usegalaxy.org.au): 151 + Tool usage (all time) - all main servers: 824 + ToolShed categories: + - Assembly + ToolShed id: merqury + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Reference-free quality, completeness, and phasing assessment + for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome + assembly projects have illumina whole genome sequencing reads available for the + assembled individual.Merqury provides a set of tools for this purpose. + bio.tool id: merqury + bio.tool ids: + - merqury + bio.tool name: Merqury +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 7 + Available on UseGalaxy.org.au: 0 + Conda id: merqury + Conda version: '1.3' + Date of first commit of the suite: '2021-04-05' + Description: Meryl a k-mer counter. + EDAM operation: + - k-mer counting + EDAM operation (no superclasses): + - k-mer counting + EDAM topic: + - Whole genome sequencing + - Genomics + - Sequence analysis + - Sequencing + EDAM topic (no superclasses): + - Whole genome sequencing + - Genomics + - Sequence analysis + Galaxy tool ids: + - meryl_arithmetic_kmers + - meryl_count_kmers + - meryl_filter_kmers + - meryl_groups_kmers + - meryl_histogram_kmers + - meryl_print + - meryl_trio_mode + Galaxy wrapper id: meryl + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl + Galaxy wrapper version: '1.3' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/marbl/meryl + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + ToolShed id: meryl + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 7 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 7 + biii: null + bio.tool description: Meryl is a tool for counting and working with sets of k-mers + that was originally developed for use in the Celera Assembler and has since been + migrated and maintained as part of Canu. + bio.tool id: meryl + bio.tool ids: + - meryl + bio.tool name: Meryl +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 1 + Conda id: metabat2 + Conda version: '2.17' + Date of first commit of the suite: '2022-01-28' + Description: MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide + frequency) is an automated metagenome binningsoftware that integrates empirical + probabilistic distances of genome abundance and tetranucleotide frequency. + EDAM operation: + - Read binning + - Sequence assembly + - Genome annotation + EDAM operation (no superclasses): + - Read binning + - Sequence assembly + - Genome annotation + EDAM topic: + - Metagenomics + - Sequence assembly + - Metagenomic sequencing + EDAM topic (no superclasses): + - Metagenomics + - Sequence assembly + - Metagenomic sequencing + Galaxy tool ids: + - metabat2_jgi_summarize_bam_contig_depths + - metabat2 + Galaxy wrapper id: metabat2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ + Galaxy wrapper version: '2.15' + No. of tool users (5 years) (usegalaxy.eu): 6135 + No. of tool users (5 years) (usegalaxy.org): 881 + No. of tool users (5 years) (usegalaxy.org.au): 1094 + No. of tool users (5 years) - all main servers: 8110 + No. of tool users (all time) (usegalaxy.eu): 6135 + No. of tool users (all time) (usegalaxy.org): 881 + No. of tool users (all time) (usegalaxy.org.au): 1094 + No. of tool users (all time) - all main servers: 8110 + Source: https://bitbucket.org/berkeleylab/metabat/src/master/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 382 + Tool usage (5 years) (usegalaxy.org): 151 + Tool usage (5 years) (usegalaxy.org.au): 104 + Tool usage (5 years) - all main servers: 637 + Tool usage (all time) (usegalaxy.eu): 382 + Tool usage (all time) (usegalaxy.org): 151 + Tool usage (all time) (usegalaxy.org.au): 104 + Tool usage (all time) - all main servers: 637 + ToolShed categories: + - Metagenomics + ToolShed id: metabat2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: an adaptive binning algorithm for robust and efficient genome + reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs + into different "bins", each of which should correspond to a putative genome | + MetaBAT2 uses nucleotide composition information and source strain abundance (measured + by depth-of-coverage by aligning the reads to the contigs) to perform binning + bio.tool id: MetaBAT_2 + bio.tool ids: + - MetaBAT_2 + bio.tool name: MetaBAT 2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: metabuli + Conda version: 1.0.8 + Date of first commit of the suite: '2024-06-04' + Description: Classifying metagenomes by jointly analysing both DNA and amino acid + (AA) sequences + EDAM operation: + - Taxonomic classification + EDAM operation (no superclasses): + - Taxonomic classification + EDAM topic: + - Taxonomy + EDAM topic (no superclasses): + - Taxonomy + Galaxy tool ids: + - metabuli_classify + Galaxy wrapper id: metabuli + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli + Galaxy wrapper version: 1.0.5 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/steineggerlab/Metabuli + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + - Metagenomics + ToolShed id: metabuli + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: 'Metabuli: specific and sensitive metagenomic classification + via joint analysis of DNA and amino acid' + bio.tool id: metabuli + bio.tool ids: + - metabuli + bio.tool name: metabuli +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: metaeuk + Conda version: 6.a5d39d9 + Date of first commit of the suite: '2020-08-04' + Description: 'MetaEuk is a modular toolkit designed for large-scale gene discovery + andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive + homology search capabilities of MMseqs2 with a dynamic programmingprocedure to + recover optimal exons sets. It reduces redundancies in multiplediscoveries of + the same gene and resolves conflicting gene predictions onthe same strand. ' + EDAM operation: + - Homology-based gene prediction + EDAM operation (no superclasses): + - Homology-based gene prediction + EDAM topic: + - Metagenomics + - Gene and protein families + EDAM topic (no superclasses): + - Metagenomics + - Gene and protein families + Galaxy tool ids: + - metaeuk_easy_predict + Galaxy wrapper id: metaeuk + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk + Galaxy wrapper version: 7.bba0d80 + No. of tool users (5 years) (usegalaxy.eu): 312 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 312 + No. of tool users (all time) (usegalaxy.eu): 312 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 312 + Source: https://github.com/soedinglab/metaeuk + Status: To update + Tool usage (5 years) (usegalaxy.eu): 40 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 40 + Tool usage (all time) (usegalaxy.eu): 40 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 40 + ToolShed categories: + - Sequence Analysis + - Genome annotation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: MetaEuk - sensitive, high-throughput gene discovery and annotation + for large-scale eukaryotic metagenomics + bio.tool id: MetaEuk + bio.tool ids: + - MetaEuk + bio.tool name: MetaEuk +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-metagenomeseq + Conda version: 1.43.0 + Date of first commit of the suite: '2017-03-27' + Description: metagenomeSeq Normalization + EDAM operation: + - Sequence visualisation + - Statistical calculation + EDAM operation (no superclasses): + - Sequence visualisation + - Statistical calculation + EDAM topic: + - Metagenomics + - Sequencing + EDAM topic (no superclasses): + - Metagenomics + - Sequencing + Galaxy tool ids: + - metagenomeseq_normalizaton + Galaxy wrapper id: metagenomeseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq + Galaxy wrapper version: 1.16.0-0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 556 + No. of tool users (5 years) (usegalaxy.org): 310 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 866 + No. of tool users (all time) (usegalaxy.eu): 756 + No. of tool users (all time) (usegalaxy.org): 514 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1270 + Source: https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 35 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 52 + Tool usage (all time) (usegalaxy.eu): 21 + Tool usage (all time) (usegalaxy.org): 55 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 76 + ToolShed categories: + - Metagenomics + ToolShed id: metagenomeseq_normalization + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Designed to determine features (be it Operational Taxanomic + Unit (OTU), species, etc.) that are differentially abundant between two or more + groups of multiple samples. It is designed to address the effects of both normalization + and under-sampling of microbial communities on disease association detection and + the testing of feature correlations. + bio.tool id: metagenomeseq + bio.tool ids: + - metagenomeseq + bio.tool name: metagenomeSeq +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 2 + Conda id: metaphlan + Conda version: 4.1.1 + Date of first commit of the suite: '2021-04-13' + Description: MetaPhlAn for Metagenomic Phylogenetic Analysis + EDAM operation: + - Nucleic acid sequence analysis + - Phylogenetic tree analysis + EDAM operation (no superclasses): + - Nucleic acid sequence analysis + EDAM topic: + - Metagenomics + - Phylogenomics + EDAM topic (no superclasses): + - Metagenomics + - Phylogenomics + Galaxy tool ids: + - customize_metaphlan_database + - extract_metaphlan_database + - merge_metaphlan_tables + - metaphlan + Galaxy wrapper id: metaphlan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ + Galaxy wrapper version: 4.1.1 + No. of tool users (5 years) (usegalaxy.eu): 16629 + No. of tool users (5 years) (usegalaxy.org): 3983 + No. of tool users (5 years) (usegalaxy.org.au): 4747 + No. of tool users (5 years) - all main servers: 25359 + No. of tool users (all time) (usegalaxy.eu): 16648 + No. of tool users (all time) (usegalaxy.org): 3983 + No. of tool users (all time) (usegalaxy.org.au): 4747 + No. of tool users (all time) - all main servers: 25378 + Source: https://github.com/biobakery/MetaPhlAn + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1183 + Tool usage (5 years) (usegalaxy.org): 572 + Tool usage (5 years) (usegalaxy.org.au): 278 + Tool usage (5 years) - all main servers: 2033 + Tool usage (all time) (usegalaxy.eu): 1187 + Tool usage (all time) (usegalaxy.org): 572 + Tool usage (all time) (usegalaxy.org.au): 278 + Tool usage (all time) - all main servers: 2037 + ToolShed categories: + - Metagenomics + ToolShed id: metaphlan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 4 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 4 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 4 + UseGalaxy.no: 4 + UseGalaxy.or: 2 + biii: null + bio.tool description: Computational tool for profiling the composition of microbial + communities from metagenomic shotgun sequencing data. + bio.tool id: metaphlan + bio.tool ids: + - metaphlan + bio.tool name: MetaPhlAn +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: metawrap-mg + Conda version: 1.3.0 + Date of first commit of the suite: '2024-04-11' + Description: A flexible pipeline for genome-resolved metagenomic data analysis + EDAM operation: + - Read binning + - Sequence assembly + - Genome annotation + - Sequence trimming + - Demultiplexing + EDAM operation (no superclasses): + - Read binning + - Sequence assembly + - Genome annotation + - Sequence trimming + - Demultiplexing + EDAM topic: + - Whole genome sequencing + - Metagenomic sequencing + - Metagenomics + EDAM topic (no superclasses): + - Whole genome sequencing + - Metagenomic sequencing + - Metagenomics + Galaxy tool ids: + - metawrapmg_binning + Galaxy wrapper id: metawrapmg + Galaxy wrapper owner: galaxy-australia + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg + Galaxy wrapper version: 1.3.0 + No. of tool users (5 years) (usegalaxy.eu): 142 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 379 + No. of tool users (5 years) - all main servers: 521 + No. of tool users (all time) (usegalaxy.eu): 142 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 379 + No. of tool users (all time) - all main servers: 521 + Source: https://github.com/bxlab/metaWRAP + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 47 + Tool usage (5 years) - all main servers: 79 + Tool usage (all time) (usegalaxy.eu): 32 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 47 + Tool usage (all time) - all main servers: 79 + ToolShed categories: + - Metagenomics + ToolShed id: metawrapmg_binning + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'MetaWRAP aims to be an easy-to-use metagenomic wrapper suite + that accomplishes the core tasks of metagenomic analysis from start to finish: + read quality control, assembly, visualization, taxonomic profiling, extracting + draft genomes (binning), and functional annotation.' + bio.tool id: metawrap + bio.tool ids: + - metawrap + bio.tool name: MetaWRAP +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mg-toolkit + Conda version: 0.10.4 + Date of first commit of the suite: '2024-07-12' + Description: Metagenomics toolkit enables scientists to download all of the sample + metadata for a given study or sequence to a single csv file. + EDAM operation: + - Data retrieval + EDAM operation (no superclasses): + - Data retrieval + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - mg_toolkit_bulk_download + - mg_toolkit_original_metadata + Galaxy wrapper id: mg_toolkit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit + Galaxy wrapper version: 0.10.4 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1 + Source: https://github.com/EBI-Metagenomics/emg-toolkit + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Metagenomics + ToolShed id: mg_toolkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + biii: null + bio.tool description: Metagenomics toolkit enables scientists to download all of + the sample metadata for a given study or sequence to a single csv file. + bio.tool id: mg-toolkit + bio.tool ids: + - mg-toolkit + bio.tool name: mg-toolkit +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2024-07-21' + Description: Select microsatellites for a bed file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - microsatbed + Galaxy wrapper id: microsatbed + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed + Galaxy wrapper version: 1.3.3 + No. of tool users (5 years) (usegalaxy.eu): 228 + No. of tool users (5 years) (usegalaxy.org): 18 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 246 + No. of tool users (all time) (usegalaxy.eu): 228 + No. of tool users (all time) (usegalaxy.org): 18 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 246 + Source: https://github.com/lmdu/pytrf + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Sequence Analysis + ToolShed id: microsatbed + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: migmap + Conda version: 1.0.3 + Date of first commit of the suite: '2017-09-29' + Description: mapper for full-length T- and B-cell repertoire sequencing + EDAM operation: + - Sequence analysis + - Read mapping + EDAM operation (no superclasses): + - Sequence analysis + - Read mapping + EDAM topic: + - Immunoproteins, genes and antigens + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - migmap + Galaxy wrapper id: migmap + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap + Galaxy wrapper version: 1.0.3 + No. of tool users (5 years) (usegalaxy.eu): 1082 + No. of tool users (5 years) (usegalaxy.org): 1153 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2235 + No. of tool users (all time) (usegalaxy.eu): 1229 + No. of tool users (all time) (usegalaxy.org): 1376 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2605 + Source: https://github.com/mikessh/migmap + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 25 + Tool usage (5 years) (usegalaxy.org): 70 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 95 + Tool usage (all time) (usegalaxy.eu): 33 + Tool usage (all time) (usegalaxy.org): 89 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 122 + ToolShed categories: + - RNA + - Sequence Analysis + ToolShed id: migmap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Mapper for full-length T- and B-cell repertoire sequencing. + bio.tool id: MiGMAP + bio.tool ids: + - MiGMAP + bio.tool name: MiGMAP +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: minia + Conda version: 3.2.6 + Date of first commit of the suite: '2020-04-08' + Description: Short-read assembler based on a de Bruijn graph + EDAM operation: + - Genome assembly + EDAM operation (no superclasses): + - Genome assembly + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - minia + Galaxy wrapper id: minia + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia + Galaxy wrapper version: 3.2.6 + No. of tool users (5 years) (usegalaxy.eu): 7116 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 278 + No. of tool users (5 years) - all main servers: 7394 + No. of tool users (all time) (usegalaxy.eu): 7116 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 278 + No. of tool users (all time) - all main servers: 7394 + Source: https://gatb.inria.fr/software/minia/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 256 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 60 + Tool usage (5 years) - all main servers: 316 + Tool usage (all time) (usegalaxy.eu): 256 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 60 + Tool usage (all time) - all main servers: 316 + ToolShed categories: + - Assembly + ToolShed id: minia + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Short-read assembler based on a de Bruijn graph, capable of + assembling a human genome on a desktop computer in a day. + bio.tool id: minia + bio.tool ids: + - minia + bio.tool name: Minia +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: miniasm + Conda version: '0.3' + Date of first commit of the suite: '2019-06-18' + Description: Miniasm - Ultrafast de novo assembly for long noisy reads (though having + no consensus step) + EDAM operation: + - De-novo assembly + EDAM operation (no superclasses): + - De-novo assembly + EDAM topic: + - Genomics + - Sequence assembly + EDAM topic (no superclasses): + - Genomics + - Sequence assembly + Galaxy tool ids: + - miniasm + Galaxy wrapper id: miniasm + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm + Galaxy wrapper version: 0.3_r179 + No. of tool users (5 years) (usegalaxy.eu): 13357 + No. of tool users (5 years) (usegalaxy.org): 8416 + No. of tool users (5 years) (usegalaxy.org.au): 898 + No. of tool users (5 years) - all main servers: 22671 + No. of tool users (all time) (usegalaxy.eu): 13479 + No. of tool users (all time) (usegalaxy.org): 8416 + No. of tool users (all time) (usegalaxy.org.au): 898 + No. of tool users (all time) - all main servers: 22793 + Source: https://github.com/lh3/miniasm + Status: To update + Tool usage (5 years) (usegalaxy.eu): 554 + Tool usage (5 years) (usegalaxy.org): 448 + Tool usage (5 years) (usegalaxy.org.au): 85 + Tool usage (5 years) - all main servers: 1087 + Tool usage (all time) (usegalaxy.eu): 562 + Tool usage (all time) (usegalaxy.org): 448 + Tool usage (all time) (usegalaxy.org.au): 85 + Tool usage (all time) - all main servers: 1095 + ToolShed categories: + - Assembly + ToolShed id: miniasm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Miniasm is a very fast OLC-based de novo assembler for noisy + long reads. It takes all-vs-all read self-mappings (typically by minimap) as input + and outputs an assembly graph in the GFA format. + bio.tool id: miniasm + bio.tool ids: + - miniasm + bio.tool name: miniasm +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: minimap2 + Conda version: '2.28' + Date of first commit of the suite: '2018-08-31' + Description: A fast pairwise aligner for genomic and spliced nucleotide sequences + EDAM operation: + - Pairwise sequence alignment + EDAM operation (no superclasses): + - Pairwise sequence alignment + EDAM topic: + - Mapping + EDAM topic (no superclasses): + - Mapping + Galaxy tool ids: + - minimap2 + Galaxy wrapper id: minimap2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 + Galaxy wrapper version: '2.28' + No. of tool users (5 years) (usegalaxy.eu): 346530 + No. of tool users (5 years) (usegalaxy.org): 108535 + No. of tool users (5 years) (usegalaxy.org.au): 22331 + No. of tool users (5 years) - all main servers: 477396 + No. of tool users (all time) (usegalaxy.eu): 349075 + No. of tool users (all time) (usegalaxy.org): 108535 + No. of tool users (all time) (usegalaxy.org.au): 22331 + No. of tool users (all time) - all main servers: 479941 + Source: https://github.com/lh3/minimap2 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4323 + Tool usage (5 years) (usegalaxy.org): 4075 + Tool usage (5 years) (usegalaxy.org.au): 1166 + Tool usage (5 years) - all main servers: 9564 + Tool usage (all time) (usegalaxy.eu): 4419 + Tool usage (all time) (usegalaxy.org): 4075 + Tool usage (all time) (usegalaxy.org.au): 1166 + Tool usage (all time) - all main servers: 9660 + ToolShed categories: + - Next Gen Mappers + ToolShed id: minimap2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Pairwise aligner for genomic and spliced nucleotide sequences + bio.tool id: minimap2 + bio.tool ids: + - minimap2 + bio.tool name: Minimap2 +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: miniprot + Conda version: '0.13' + Date of first commit of the suite: '2023-03-23' + Description: Align a protein sequence against a genome with affine gap penalty, + splicing and frameshift. + EDAM operation: + - Sequence alignment + - Protein sequence analysis + EDAM operation (no superclasses): + - Sequence alignment + - Protein sequence analysis + EDAM topic: + - Sequence sites, features and motifs + - Sequence analysis + EDAM topic (no superclasses): + - Sequence sites, features and motifs + - Sequence analysis + Galaxy tool ids: + - miniprot + - miniprot_index + Galaxy wrapper id: miniprot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot + Galaxy wrapper version: '0.13' + No. of tool users (5 years) (usegalaxy.eu): 1244 + No. of tool users (5 years) (usegalaxy.org): 24 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1268 + No. of tool users (all time) (usegalaxy.eu): 1244 + No. of tool users (all time) (usegalaxy.org): 24 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1268 + Source: https://github.com/lh3/miniprot + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 86 + Tool usage (5 years) (usegalaxy.org): 15 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 101 + Tool usage (all time) (usegalaxy.eu): 86 + Tool usage (all time) (usegalaxy.org): 15 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 101 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Miniprot aligns a protein sequence against a genome with affine + gap penalty, splicing and frameshift. It is primarily intended for annotating + protein-coding genes in a new species using known genes from other species. + bio.tool id: miniprot + bio.tool ids: + - miniprot + bio.tool name: miniprot +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mirmachine + Conda version: 0.2.13 + Date of first commit of the suite: '2024-03-15' + Description: Tool to detect miRNA in genome sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mirmachine + Galaxy wrapper id: mirmachine + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine + Galaxy wrapper version: 0.2.13 + No. of tool users (5 years) (usegalaxy.eu): 2 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2 + No. of tool users (all time) (usegalaxy.eu): 2 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2 + Source: https://github.com/sinanugur/MirMachine + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Sequence Analysis + ToolShed id: mirmachine + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mirnature + Conda version: '1.1' + Date of first commit of the suite: '2022-12-11' + Description: Computational detection of canonical microRNAs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mirnature + Galaxy wrapper id: mirnature + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature + Galaxy wrapper source: https://github.com/Bierinformatik/miRNAture + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 18 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 18 + No. of tool users (all time) (usegalaxy.eu): 18 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 18 + Source: https://github.com/Bierinformatik/miRNAture + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - RNA + - Sequence Analysis + ToolShed id: mirnature + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: mitobim + Conda version: 1.9.1 + Date of first commit of the suite: '2020-12-29' + Description: assemble mitochondrial genomes + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mitobim + Galaxy wrapper id: mitobim + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim + Galaxy wrapper version: 1.9.1 + No. of tool users (5 years) (usegalaxy.eu): 1117 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 295 + No. of tool users (5 years) - all main servers: 1412 + No. of tool users (all time) (usegalaxy.eu): 1117 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 295 + No. of tool users (all time) - all main servers: 1412 + Source: https://github.com/chrishah/MITObim + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 116 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 25 + Tool usage (5 years) - all main servers: 141 + Tool usage (all time) (usegalaxy.eu): 116 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 25 + Tool usage (all time) - all main servers: 141 + ToolShed categories: + - Assembly + ToolShed id: mitobim + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: mitos + Conda version: 2.1.9 + Date of first commit of the suite: '2020-02-18' + Description: de-novo annotation of metazoan mitochondrial genomes + EDAM operation: + - Genome annotation + EDAM operation (no superclasses): + - Genome annotation + EDAM topic: + - Zoology + - Whole genome sequencing + EDAM topic (no superclasses): + - Zoology + - Whole genome sequencing + Galaxy tool ids: + - mitos + - mitos2 + Galaxy wrapper id: mitos + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos + Galaxy wrapper version: 1.1.7 + No. of tool users (5 years) (usegalaxy.eu): 191295 + No. of tool users (5 years) (usegalaxy.org): 42265 + No. of tool users (5 years) (usegalaxy.org.au): 10904 + No. of tool users (5 years) - all main servers: 244464 + No. of tool users (all time) (usegalaxy.eu): 191295 + No. of tool users (all time) (usegalaxy.org): 42265 + No. of tool users (all time) (usegalaxy.org.au): 10904 + No. of tool users (all time) - all main servers: 244464 + Source: http://mitos.bioinf.uni-leipzig.de/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1111 + Tool usage (5 years) (usegalaxy.org): 320 + Tool usage (5 years) (usegalaxy.org.au): 83 + Tool usage (5 years) - all main servers: 1514 + Tool usage (all time) (usegalaxy.eu): 1111 + Tool usage (all time) (usegalaxy.org): 320 + Tool usage (all time) (usegalaxy.org.au): 83 + Tool usage (all time) - all main servers: 1514 + ToolShed categories: + - Sequence Analysis + ToolShed id: mitos + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: De novo metazoan mitochondrial genome annotation. + bio.tool id: mitos + bio.tool ids: + - mitos + bio.tool name: MITOS +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: mlst + Conda version: 2.23.0 + Date of first commit of the suite: '2016-12-12' + Description: Scan contig files against PubMLST typing schemes + EDAM operation: + - Multilocus sequence typing + EDAM operation (no superclasses): + - Multilocus sequence typing + EDAM topic: + - Immunoproteins and antigens + EDAM topic (no superclasses): + - Immunoproteins and antigens + Galaxy tool ids: + - mlst + - mlst_list + Galaxy wrapper id: mlst + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst + Galaxy wrapper version: 2.22.0 + No. of tool users (5 years) (usegalaxy.eu): 13300 + No. of tool users (5 years) (usegalaxy.org): 6532 + No. of tool users (5 years) (usegalaxy.org.au): 10334 + No. of tool users (5 years) - all main servers: 30166 + No. of tool users (all time) (usegalaxy.eu): 13471 + No. of tool users (all time) (usegalaxy.org): 6532 + No. of tool users (all time) (usegalaxy.org.au): 11841 + No. of tool users (all time) - all main servers: 31844 + Source: https://github.com/tseemann/mlst + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1480 + Tool usage (5 years) (usegalaxy.org): 1167 + Tool usage (5 years) (usegalaxy.org.au): 1083 + Tool usage (5 years) - all main servers: 3730 + Tool usage (all time) (usegalaxy.eu): 1501 + Tool usage (all time) (usegalaxy.org): 1167 + Tool usage (all time) (usegalaxy.org.au): 1300 + Tool usage (all time) - all main servers: 3968 + ToolShed categories: + - Sequence Analysis + ToolShed id: mlst + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Multi Locus Sequence Typing from an assembled genome or from + a set of reads. + bio.tool id: mlst + bio.tool ids: + - mlst + bio.tool name: MLST +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: moabs + Conda version: 1.3.9.0 + Date of first commit of the suite: '2019-07-28' + Description: MOABS for differential methylation analysis on Bisulfite sequencing + data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - moabs + Galaxy wrapper id: moabs + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs + Galaxy wrapper source: https://github.com/sunnyisgalaxy/moabs + Galaxy wrapper version: 1.3.4.6 + No. of tool users (5 years) (usegalaxy.eu): 339 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 339 + No. of tool users (all time) (usegalaxy.eu): 339 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 339 + Source: https://github.com/sunnyisgalaxy/moabs + Status: To update + Tool usage (5 years) (usegalaxy.eu): 56 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 56 + Tool usage (all time) (usegalaxy.eu): 56 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 56 + ToolShed categories: + - Epigenetics + ToolShed id: moabs + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: mosdepth + Conda version: 0.3.8 + Date of first commit of the suite: '2022-12-04' + Description: fast and flexible BAM/CRAM depth calculation + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mosdepth + Galaxy wrapper id: mosdepth + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth + Galaxy wrapper version: 0.3.8 + No. of tool users (5 years) (usegalaxy.eu): 1278 + No. of tool users (5 years) (usegalaxy.org): 168 + No. of tool users (5 years) (usegalaxy.org.au): 102 + No. of tool users (5 years) - all main servers: 1548 + No. of tool users (all time) (usegalaxy.eu): 1278 + No. of tool users (all time) (usegalaxy.org): 168 + No. of tool users (all time) (usegalaxy.org.au): 102 + No. of tool users (all time) - all main servers: 1548 + Source: https://github.com/brentp/mosdepth + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 87 + Tool usage (5 years) (usegalaxy.org): 24 + Tool usage (5 years) (usegalaxy.org.au): 5 + Tool usage (5 years) - all main servers: 116 + Tool usage (all time) (usegalaxy.eu): 87 + Tool usage (all time) (usegalaxy.org): 24 + Tool usage (all time) (usegalaxy.org.au): 5 + Tool usage (all time) - all main servers: 116 + ToolShed categories: + - SAM + ToolShed id: mosdepth + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 129 + Available on UseGalaxy.fr: 129 + Available on UseGalaxy.org (Main): 129 + Available on UseGalaxy.org.au: 129 + Conda id: mothur + Conda version: 1.48.0 + Date of first commit of the suite: '2018-08-03' + Description: Mothur wrappers + EDAM operation: + - DNA barcoding + - Sequencing quality control + - Sequence clustering + - Taxonomic classification + - Visualisation + - Sequence read processing + - Phylogenetic analysis + EDAM operation (no superclasses): + - DNA barcoding + - Sequencing quality control + - Sequence clustering + - Taxonomic classification + - Visualisation + - Sequence read processing + - Phylogenetic analysis + EDAM topic: + - Microbial ecology + - Taxonomy + - Sequence analysis + - Phylogeny + EDAM topic (no superclasses): + - Microbial ecology + - Taxonomy + - Sequence analysis + - Phylogeny + Galaxy tool ids: + - mothur_align_check + - mothur_align_seqs + - mothur_amova + - mothur_anosim + - mothur_bin_seqs + - mothur_biom_info + - mothur_chimera_bellerophon + - mothur_chimera_ccode + - mothur_chimera_check + - mothur_chimera_perseus + - mothur_chimera_pintail + - mothur_chimera_slayer + - mothur_chimera_uchime + - mothur_chimera_vsearch + - mothur_chop_seqs + - mothur_classify_otu + - mothur_classify_seqs + - mothur_classify_tree + - mothur_clearcut + - mothur_cluster_classic + - mothur_cluster_fragments + - mothur_cluster_split + - mothur_cluster + - mothur_collect_shared + - mothur_collect_single + - mothur_consensus_seqs + - mothur_cooccurrence + - mothur_corr_axes + - mothur_count_groups + - mothur_count_seqs + - mothur_create_database + - mothur_degap_seqs + - mothur_deunique_seqs + - mothur_deunique_tree + - mothur_dist_seqs + - mothur_dist_shared + - mothur_fastq_info + - mothur_filter_seqs + - mothur_filter_shared + - mothur_get_communitytype + - mothur_get_coremicrobiome + - mothur_get_dists + - mothur_get_group + - mothur_get_groups + - mothur_get_label + - mothur_get_lineage + - mothur_get_mimarkspackage + - mothur_get_otulabels + - mothur_get_otulist + - mothur_get_oturep + - mothur_get_otus + - mothur_get_rabund + - mothur_get_relabund + - mothur_get_sabund + - mothur_get_seqs + - mothur_get_sharedseqs + - mothur_heatmap_bin + - mothur_heatmap_sim + - mothur_homova + - mothur_indicator + - mothur_lefse + - mothur_libshuff + - mothur_list_otulabels + - mothur_list_seqs + - mothur_make_biom + - mothur_make_contigs + - mothur_make_design + - mothur_make_fastq + - mothur_make_group + - mothur_make_lefse + - mothur_make_lookup + - mothur_make_shared + - mothur_make_sra + - mothur_mantel + - mothur_merge_count + - mothur_merge_files + - mothur_merge_groups + - mothur_merge_sfffiles + - mothur_merge_taxsummary + - mothur_metastats + - mothur_mimarks_attributes + - mothur_nmds + - mothur_normalize_shared + - mothur_otu_association + - mothur_otu_hierarchy + - mothur_pairwise_seqs + - mothur_parse_list + - mothur_parsimony + - mothur_pca + - mothur_pcoa + - mothur_pcr_seqs + - mothur_phylo_diversity + - mothur_phylotype + - mothur_pre_cluster + - mothur_primer_design + - mothur_rarefaction_shared + - mothur_rarefaction_single + - mothur_remove_dists + - mothur_remove_groups + - mothur_remove_lineage + - mothur_remove_otulabels + - mothur_remove_otus + - mothur_remove_rare + - mothur_remove_seqs + - mothur_rename_seqs + - mothur_reverse_seqs + - mothur_screen_seqs + - mothur_sens_spec + - mothur_seq_error + - mothur_sffinfo + - mothur_shhh_flows + - mothur_shhh_seqs + - mothur_sort_seqs + - mothur_split_abund + - mothur_split_groups + - mothur_sub_sample + - mothur_summary_qual + - mothur_summary_seqs + - mothur_summary_shared + - mothur_summary_single + - mothur_summary_tax + - mothur_taxonomy_to_krona + - mothur_tree_shared + - mothur_trim_flows + - mothur_trim_seqs + - mothur_unifrac_unweighted + - mothur_unifrac_weighted + - mothur_unique_seqs + - mothur_venn + Galaxy wrapper id: mothur + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 297546 + No. of tool users (5 years) (usegalaxy.org): 565218 + No. of tool users (5 years) (usegalaxy.org.au): 167400 + No. of tool users (5 years) - all main servers: 1030164 + No. of tool users (all time) (usegalaxy.eu): 326056 + No. of tool users (all time) (usegalaxy.org): 682083 + No. of tool users (all time) (usegalaxy.org.au): 182490 + No. of tool users (all time) - all main servers: 1190629 + Source: https://www.mothur.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 37506 + Tool usage (5 years) (usegalaxy.org): 72163 + Tool usage (5 years) (usegalaxy.org.au): 26963 + Tool usage (5 years) - all main servers: 136632 + Tool usage (all time) (usegalaxy.eu): 41763 + Tool usage (all time) (usegalaxy.org): 89926 + Tool usage (all time) (usegalaxy.org.au): 28404 + Tool usage (all time) - all main servers: 160093 + ToolShed categories: + - Metagenomics + ToolShed id: mothur + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 128 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 126 + Tools available on UseGalaxy.cz: 129 + Tools available on UseGalaxy.eu: 129 + Tools available on UseGalaxy.fr: 129 + Tools available on UseGalaxy.no: 129 + Tools available on UseGalaxy.org (Main): 129 + Tools available on UseGalaxy.org.au: 129 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 126 + UseGalaxy.cz: 129 + UseGalaxy.eu: 129 + UseGalaxy.fr: 3 + UseGalaxy.no: 129 + UseGalaxy.or: 129 + biii: null + bio.tool description: Open-source, platform-independent, community-supported software + for describing and comparing microbial communities + bio.tool id: mothur + bio.tool ids: + - mothur + bio.tool name: mothur +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: msaboot + Conda version: 0.1.2 + Date of first commit of the suite: '2018-02-12' + Description: A multiple sequences alignment bootstrapping tool. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - msaboot + Galaxy wrapper id: msaboot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 864 + No. of tool users (5 years) (usegalaxy.org): 1100 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1964 + No. of tool users (all time) (usegalaxy.eu): 929 + No. of tool users (all time) (usegalaxy.org): 1100 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2029 + Source: https://github.com/phac-nml/msaboot + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 91 + Tool usage (5 years) (usegalaxy.org): 175 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 266 + Tool usage (all time) (usegalaxy.eu): 101 + Tool usage (all time) (usegalaxy.org): 175 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 276 + ToolShed categories: + - Fasta Manipulation + ToolShed id: msaboot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: fonts-conda-ecosystem + Conda version: null + Date of first commit of the suite: '2017-03-06' + Description: Analyzes collections of multi-condition ChIP-seq data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - multigps + Galaxy wrapper id: multigps + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps + Galaxy wrapper version: 0.74.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 485 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 485 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 871 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 871 + Source: http://mahonylab.org/software/multigps/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 159 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 159 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 298 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 298 + ToolShed categories: + - ChIP-seq + ToolShed id: multigps + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-multigsea + Conda version: 1.12.0 + Date of first commit of the suite: '2023-06-07' + Description: GSEA-based pathway enrichment analysis for multi-omics data + EDAM operation: + - Gene-set enrichment analysis + - Aggregation + - Pathway analysis + EDAM operation (no superclasses): + - Gene-set enrichment analysis + - Aggregation + - Pathway analysis + EDAM topic: + - Metabolomics + - Molecular interactions, pathways and networks + - Proteomics + - Transcriptomics + - Small molecules + EDAM topic (no superclasses): + - Metabolomics + - Molecular interactions, pathways and networks + - Proteomics + - Transcriptomics + - Small molecules + Galaxy tool ids: + - multigsea + Galaxy wrapper id: multigsea + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea + Galaxy wrapper version: 1.12.0 + No. of tool users (5 years) (usegalaxy.eu): 106 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 106 + No. of tool users (all time) (usegalaxy.eu): 106 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 106 + Source: https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 25 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 25 + Tool usage (all time) (usegalaxy.eu): 25 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 25 + ToolShed categories: + - Transcriptomics + - Proteomics + - Statistics + ToolShed id: multigsea + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: 'A GSEA-based pathway enrichment analysis for multi-omics + data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, + BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with + multi omics data integration.' + bio.tool id: multiGSEA + bio.tool ids: + - multiGSEA + bio.tool name: multiGSEA +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: multiqc + Conda version: 1.25.1 + Date of first commit of the suite: '2020-04-28' + Description: MultiQC aggregates results from bioinformatics analyses across many + samples into a single report + EDAM operation: + - Validation + - Sequencing quality control + EDAM operation (no superclasses): + - Sequencing quality control + EDAM topic: + - Sequencing + - Bioinformatics + - Sequence analysis + - Genomics + EDAM topic (no superclasses): + - Sequencing + - Bioinformatics + - Sequence analysis + - Genomics + Galaxy tool ids: + - multiqc + Galaxy wrapper id: multiqc + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc + Galaxy wrapper version: 1.24.1 + No. of tool users (5 years) (usegalaxy.eu): 182221 + No. of tool users (5 years) (usegalaxy.org): 163961 + No. of tool users (5 years) (usegalaxy.org.au): 40663 + No. of tool users (5 years) - all main servers: 386845 + No. of tool users (all time) (usegalaxy.eu): 192389 + No. of tool users (all time) (usegalaxy.org): 182413 + No. of tool users (all time) (usegalaxy.org.au): 41855 + No. of tool users (all time) - all main servers: 416657 + Source: http://multiqc.info/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 19343 + Tool usage (5 years) (usegalaxy.org): 26449 + Tool usage (5 years) (usegalaxy.org.au): 5974 + Tool usage (5 years) - all main servers: 51766 + Tool usage (all time) (usegalaxy.eu): 20494 + Tool usage (all time) (usegalaxy.org): 29758 + Tool usage (all time) (usegalaxy.org.au): 6157 + Tool usage (all time) - all main servers: 56409 + ToolShed categories: + - Fastq Manipulation + - Statistics + - Visualization + ToolShed id: multiqc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: MultiQC aggregates results from multiple bioinformatics analyses + across many samples into a single report. It searches a given directory for analysis + logs and compiles a HTML report. It's a general use tool, perfect for summarising + the output from numerous bioinformatics tools. + bio.tool id: multiqc + bio.tool ids: + - multiqc + bio.tool name: MultiQC +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 6 + Available on UseGalaxy.org (Main): 6 + Available on UseGalaxy.org.au: 6 + Conda id: mummer4 + Conda version: 4.0.0rc1 + Date of first commit of the suite: '2018-06-30' + Description: Mummer4 Tools + EDAM operation: + - Multiple sequence alignment + EDAM operation (no superclasses): + - Multiple sequence alignment + EDAM topic: + - Sequence analysis + - Human genetics + EDAM topic (no superclasses): + - Sequence analysis + - Human genetics + Galaxy tool ids: + - mummer_delta_filter + - mummer_dnadiff + - mummer_mummer + - mummer_mummerplot + - mummer_nucmer + - mummer_show_coords + Galaxy wrapper id: mummer4 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 + Galaxy wrapper version: 4.0.0rc1 + No. of tool users (5 years) (usegalaxy.eu): 21587 + No. of tool users (5 years) (usegalaxy.org): 29284 + No. of tool users (5 years) (usegalaxy.org.au): 8194 + No. of tool users (5 years) - all main servers: 59065 + No. of tool users (all time) (usegalaxy.eu): 22119 + No. of tool users (all time) (usegalaxy.org): 29284 + No. of tool users (all time) (usegalaxy.org.au): 8194 + No. of tool users (all time) - all main servers: 59597 + Source: https://github.com/mummer4/mummer + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1940 + Tool usage (5 years) (usegalaxy.org): 3626 + Tool usage (5 years) (usegalaxy.org.au): 545 + Tool usage (5 years) - all main servers: 6111 + Tool usage (all time) (usegalaxy.eu): 2033 + Tool usage (all time) (usegalaxy.org): 3626 + Tool usage (all time) (usegalaxy.org.au): 545 + Tool usage (all time) - all main servers: 6204 + ToolShed categories: + - Sequence Analysis + ToolShed id: mummer4 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 6 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 6 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 6 + Tools available on UseGalaxy.no: 6 + Tools available on UseGalaxy.org (Main): 6 + Tools available on UseGalaxy.org.au: 6 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 6 + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.fr: 3 + UseGalaxy.no: 6 + UseGalaxy.or: 6 + biii: null + bio.tool description: System for rapidly aligning large DNA sequences to one another. + bio.tool id: mummer4 + bio.tool ids: + - mummer4 + bio.tool name: MUMmer4 +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mykrobe + Conda version: 0.13.0 + Date of first commit of the suite: '2017-12-18' + Description: Antibiotic resistance predictions + EDAM operation: + - Antimicrobial resistance prediction + - Variant calling + - Genotyping + - Sequence trimming + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + - Variant calling + - Genotyping + - Sequence trimming + EDAM topic: + - Whole genome sequencing + - Genotype and phenotype + - Probes and primers + - Genetic variation + - Metagenomics + EDAM topic (no superclasses): + - Whole genome sequencing + - Genotype and phenotype + - Probes and primers + - Genetic variation + - Metagenomics + Galaxy tool ids: + - mykrobe_predict + Galaxy wrapper id: mykrobe + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe + Galaxy wrapper version: 0.10.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/Mykrobe-tools/mykrobe + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: mykrobe + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: Antibiotic resistance prediction for Mycobacterium tuberculosis + from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table + of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting + to install with bioconda, please ensure you have your channels set up as specified + in the documentation. If you don't, you may run into issues with an older version + of mykrobe being installed + bio.tool id: Mykrobe + bio.tool ids: + - Mykrobe + bio.tool name: Mykrobe +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mzmine + Conda version: 3.9.0 + Date of first commit of the suite: '2023-10-21' + Description: mass-spectrometry data processing, with the main focus on LC-MS data + EDAM operation: + - Natural product identification + - Standardisation and normalisation + - Peptide database search + - Deisotoping + - Clustering + - Filtering + - Chromatographic alignment + - Peak detection + - Peptide identification + - Chromatogram visualisation + - Mass spectrum visualisation + - Structure visualisation + - Plotting + - Heat map generation + EDAM operation (no superclasses): + - Natural product identification + - Standardisation and normalisation + - Peptide database search + - Deisotoping + - Clustering + - Filtering + - Chromatographic alignment + - Peak detection + - Peptide identification + - Chromatogram visualisation + - Mass spectrum visualisation + - Structure visualisation + - Plotting + - Heat map generation + EDAM topic: + - Proteomics + - Metabolomics + - Proteomics experiment + - Small molecules + EDAM topic (no superclasses): + - Proteomics + - Metabolomics + - Proteomics experiment + - Small molecules + Galaxy tool ids: + - mzmine_batch + Galaxy wrapper id: mzmine + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine + Galaxy wrapper source: https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ + Galaxy wrapper version: 3.9.0 + No. of tool users (5 years) (usegalaxy.eu): 9 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 9 + No. of tool users (all time) (usegalaxy.eu): 9 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 9 + Source: http://mzmine.github.io/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Metabolomics + ToolShed id: mzmine_batch + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Toolbox for visualization and analysis of LC-MS data in netCDF + or mzXML. + bio.tool id: mzmine + bio.tool ids: + - mzmine + bio.tool name: MZmine +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 0 + Conda id: naltorfs + Conda version: 0.1.2 + Date of first commit of the suite: '2022-04-11' + Description: 'nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bicodon_counts_from_fasta + - codon_freq_from_bicodons + - find_nested_alt_orfs + Galaxy wrapper id: naltorfs + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 204 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 204 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 204 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 204 + Source: https://github.com/BlankenbergLab/nAltORFs + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 75 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 75 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 75 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 75 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: nanocompore + Conda version: 1.0.4 + Date of first commit of the suite: '2020-05-01' + Description: Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets + from different experimental conditions expected to have a significant impact on + RNA modifications. It is recommended to have at least 2 replicates per condition. + For example one can use a control condition with a significantly reduced number + of modifications such as a cell line for which a modification writing enzyme was + knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of + interests could be synthesized in-vitro. + EDAM operation: + - Post-translation modification site prediction + - PolyA signal detection + - Genotyping + - k-mer counting + EDAM operation (no superclasses): + - PolyA signal detection + - Genotyping + - k-mer counting + EDAM topic: + - Functional, regulatory and non-coding RNA + - RNA-Seq + - Gene transcripts + - Transcriptomics + - Transcription factors and regulatory sites + EDAM topic (no superclasses): + - Functional, regulatory and non-coding RNA + - RNA-Seq + - Gene transcripts + - Transcriptomics + - Transcription factors and regulatory sites + Galaxy tool ids: + - nanocompore_db + - nanocompore_sampcomp + Galaxy wrapper id: nanocompore + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore + Galaxy wrapper version: 1.0.0rc3.post2 + No. of tool users (5 years) (usegalaxy.eu): 839 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 269 + No. of tool users (5 years) - all main servers: 1108 + No. of tool users (all time) (usegalaxy.eu): 839 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 269 + No. of tool users (all time) - all main servers: 1108 + Source: https://nanocompore.rna.rocks/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 12 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 5 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 5 + Tool usage (all time) - all main servers: 17 + ToolShed categories: + - Sequence Analysis + ToolShed id: nanocompore + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.no: 2 + UseGalaxy.or: 1 + biii: null + bio.tool description: RNA modifications detection by comparative Nanopore direct + RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore + identifies differences in ONT nanopore sequencing raw signal corresponding to + RNA modifications by comparing 2 samples.Analyses performed for the nanocompore + paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from + different experimental conditions expected to have a significant impact on RNA + modifications. It is recommended to have at least 2 replicates per condition. + For example one can use a control condition with a significantly reduced number + of modifications such as a cell line for which a modification writing enzyme was + knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of + interests could be synthesized in-vitro + bio.tool id: Nanocompore + bio.tool ids: + - Nanocompore + bio.tool name: Nanocompore +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: nanoplot + Conda version: 1.43.0 + Date of first commit of the suite: '2018-09-28' + Description: Plotting tool for long read sequencing data and alignments + EDAM operation: + - Scatter plot plotting + - Box-Whisker plot plotting + EDAM operation (no superclasses): + - Scatter plot plotting + - Box-Whisker plot plotting + EDAM topic: + - Genomics + EDAM topic (no superclasses): + - Genomics + Galaxy tool ids: + - nanoplot + Galaxy wrapper id: nanoplot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ + Galaxy wrapper version: 1.43.0 + No. of tool users (5 years) (usegalaxy.eu): 99052 + No. of tool users (5 years) (usegalaxy.org): 40386 + No. of tool users (5 years) (usegalaxy.org.au): 17919 + No. of tool users (5 years) - all main servers: 157357 + No. of tool users (all time) (usegalaxy.eu): 100009 + No. of tool users (all time) (usegalaxy.org): 40386 + No. of tool users (all time) (usegalaxy.org.au): 17919 + No. of tool users (all time) - all main servers: 158314 + Source: https://github.com/wdecoster/NanoPlot + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 5671 + Tool usage (5 years) (usegalaxy.org): 3371 + Tool usage (5 years) (usegalaxy.org.au): 2188 + Tool usage (5 years) - all main servers: 11230 + Tool usage (all time) (usegalaxy.eu): 5755 + Tool usage (all time) (usegalaxy.org): 3371 + Tool usage (all time) (usegalaxy.org.au): 2188 + Tool usage (all time) - all main servers: 11314 + ToolShed categories: + - Visualization + ToolShed id: nanoplot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: NanoPlot is a tool with various visualizations of sequencing + data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended + for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences + bio.tool id: nanoplot + bio.tool ids: + - nanoplot + bio.tool name: NanoPlot +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: nanopolishcomp + Conda version: 0.6.12 + Date of first commit of the suite: '2020-04-27' + Description: NanopolishComp contains 2 modules. Eventalign_collapse collapses the + raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate + methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. + EDAM operation: + - Methylation analysis + - Collapsing methods + EDAM operation (no superclasses): + - Methylation analysis + - Collapsing methods + EDAM topic: + - Sequence analysis + - Sequencing + - Genetic variation + EDAM topic (no superclasses): + - Sequence analysis + - Sequencing + - Genetic variation + Galaxy tool ids: + - nanopolishcomp_eventaligncollapse + - nanopolishcomp_freqmethcalculate + Galaxy wrapper id: nanopolishcomp + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp + Galaxy wrapper version: 0.6.11 + No. of tool users (5 years) (usegalaxy.eu): 1091 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1091 + No. of tool users (all time) (usegalaxy.eu): 1091 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1091 + Source: https://a-slide.github.io/NanopolishComp + Status: To update + Tool usage (5 years) (usegalaxy.eu): 44 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 44 + Tool usage (all time) (usegalaxy.eu): 44 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 44 + ToolShed categories: + - Sequence Analysis + ToolShed id: nanopolishcomp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + biii: null + bio.tool description: NanopolishComp is a Python3 package for downstream analyses + of Nanopolish output files.It is a companion package for Nanopolish. + bio.tool id: nanopolishcomp + bio.tool ids: + - nanopolishcomp + bio.tool name: NanopolishComp +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: ncbi-acc-download + Conda version: 0.2.8 + Date of first commit of the suite: '2019-11-07' + Description: Download sequences from GenBank/RefSeq by accession through the NCBI + ENTREZ API + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ncbi_acc_download + Galaxy wrapper id: ncbi_acc_download + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download + Galaxy wrapper version: 0.2.8 + No. of tool users (5 years) (usegalaxy.eu): 6873 + No. of tool users (5 years) (usegalaxy.org): 17651 + No. of tool users (5 years) (usegalaxy.org.au): 6228 + No. of tool users (5 years) - all main servers: 30752 + No. of tool users (all time) (usegalaxy.eu): 6873 + No. of tool users (all time) (usegalaxy.org): 17651 + No. of tool users (all time) (usegalaxy.org.au): 6228 + No. of tool users (all time) - all main servers: 30752 + Source: https://github.com/kblin/ncbi-acc-download + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1664 + Tool usage (5 years) (usegalaxy.org): 4513 + Tool usage (5 years) (usegalaxy.org.au): 972 + Tool usage (5 years) - all main servers: 7149 + Tool usage (all time) (usegalaxy.eu): 1664 + Tool usage (all time) (usegalaxy.org): 4513 + Tool usage (all time) (usegalaxy.org.au): 972 + Tool usage (all time) - all main servers: 7149 + ToolShed categories: + - Data Source + ToolShed id: ncbi_acc_download + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: ncbi-datasets-cli + Conda version: null + Date of first commit of the suite: '2022-06-23' + Description: NCBI datasets downloads biological sequence data across all domains + of life from NCBI. + EDAM operation: + - Data handling + - Sequence database search + - Data retrieval + EDAM operation (no superclasses): + - Data handling + - Sequence database search + - Data retrieval + EDAM topic: + - Biological databases + EDAM topic (no superclasses): + - Biological databases + Galaxy tool ids: + - datasets_download_gene + - datasets_download_genome + Galaxy wrapper id: ncbi_datasets + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets + Galaxy wrapper version: 16.20.0 + No. of tool users (5 years) (usegalaxy.eu): 4417 + No. of tool users (5 years) (usegalaxy.org): 6940 + No. of tool users (5 years) (usegalaxy.org.au): 1 + No. of tool users (5 years) - all main servers: 11358 + No. of tool users (all time) (usegalaxy.eu): 4417 + No. of tool users (all time) (usegalaxy.org): 6940 + No. of tool users (all time) (usegalaxy.org.au): 1 + No. of tool users (all time) - all main servers: 11358 + Source: https://github.com/ncbi/datasets + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1024 + Tool usage (5 years) (usegalaxy.org): 2275 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 3300 + Tool usage (all time) (usegalaxy.eu): 1024 + Tool usage (all time) (usegalaxy.org): 2275 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 3300 + ToolShed categories: + - Data Source + ToolShed id: ncbi_datasets + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: NCBI Datasets is a new resource that lets you easily gather + data from across NCBI databases. Find and download sequence, annotation, and metadata + for genes and genomes using our command-line tools or web interface. + bio.tool id: ncbi_datasets + bio.tool ids: + - ncbi_datasets + bio.tool name: NCBI Datasets +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: entrez-direct + Conda version: '22.4' + Date of first commit of the suite: '2022-03-22' + Description: NCBI Entrez Direct allow fetching data from NCBI Databases + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ncbi_entrez_direct_efetch + - ncbi_entrez_direct_einfo + - ncbi_entrez_direct_esearch + Galaxy wrapper id: ncbi_entrez_direct + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct + Galaxy wrapper version: '22.4' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 3 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3 + Source: http://www.ncbi.nlm.nih.gov/books/NBK179288/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Data Source + ToolShed id: ncbi_entrez_direct + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2020-08-07' + Description: NCBI Entrez E-Utilties allow fetching data from NCBI Databases + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ncbi_eutils_ecitmatch + - ncbi_eutils_efetch + - ncbi_eutils_einfo + - ncbi_eutils_elink + - ncbi_eutils_epost + - ncbi_eutils_esearch + - ncbi_eutils_esummary + Galaxy wrapper id: ncbi_entrez_eutils + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils + Galaxy wrapper version: '1.70' + No. of tool users (5 years) (usegalaxy.eu): 2794 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2794 + No. of tool users (all time) (usegalaxy.eu): 3191 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3191 + Source: https://www.ncbi.nlm.nih.gov/books/NBK25501/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 533 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 533 + Tool usage (all time) (usegalaxy.eu): 664 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 664 + ToolShed categories: + - Data Source + ToolShed id: ncbi_entrez_eutils + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 4 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 4 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 7 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + UseGalaxy.fr: 2 + UseGalaxy.no: 7 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: ncbi-fcs-gx + Conda version: 0.5.4 + Date of first commit of the suite: '2023-11-14' + Description: FCS-GX detects contamination from foreign organisms in genome sequences + using the genome cross-species aligner (GX). + EDAM operation: + - Sequence assembly validation + - Sequence trimming + - Sequence contamination filtering + EDAM operation (no superclasses): + - Sequence assembly validation + - Sequence trimming + - Sequence contamination filtering + EDAM topic: + - Sequence analysis + - Sequence assembly + EDAM topic (no superclasses): + - Sequence analysis + - Sequence assembly + Galaxy tool ids: + - ncbi_fcs_gx + Galaxy wrapper id: ncbi_fcs_gx + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx + Galaxy wrapper version: 0.5.4 + No. of tool users (5 years) (usegalaxy.eu): 125 + No. of tool users (5 years) (usegalaxy.org): 2489 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2614 + No. of tool users (all time) (usegalaxy.eu): 125 + No. of tool users (all time) (usegalaxy.org): 2489 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2614 + Source: https://github.com/ncbi/fcs-gx + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 26 + Tool usage (5 years) (usegalaxy.org): 139 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 165 + Tool usage (all time) (usegalaxy.eu): 26 + Tool usage (all time) (usegalaxy.org): 139 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 165 + ToolShed categories: + - Sequence Analysis + ToolShed id: ncbi_fcs_gx + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: The NCBI Foreign Contamination Screen (FCS) is a tool suite + for identifying and removing contaminant sequences in genome assemblies. Contaminants + are defined as sequences in a dataset that do not originate from the biological + source organism and can arise from a variety of environmental and laboratory sources. + FCS will help you remove contaminants from genomes before submission to GenBank. + bio.tool id: ncbi_fcs + bio.tool ids: + - ncbi_fcs + bio.tool name: NCBI fcs +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: necat + Conda version: 0.0.1_update20200803 + Date of first commit of the suite: '2021-11-29' + Description: Error correction and de-novo assembly for ONT Nanopore reads + EDAM operation: + - De-novo assembly + EDAM operation (no superclasses): + - De-novo assembly + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - necat + Galaxy wrapper id: necat + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat + Galaxy wrapper version: 0.0.1_update20200803 + No. of tool users (5 years) (usegalaxy.eu): 790 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 790 + No. of tool users (all time) (usegalaxy.eu): 790 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 790 + Source: https://github.com/xiaochuanle/NECAT + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 160 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 160 + Tool usage (all time) (usegalaxy.eu): 160 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 160 + ToolShed categories: + - Assembly + ToolShed id: necat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: NECAT is an error correction and de-novo assembly tool for + Nanopore long noisy reads. + bio.tool id: necat + bio.tool ids: + - necat + bio.tool name: NECAT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: newick_utils + Conda version: '1.6' + Date of first commit of the suite: '2018-10-01' + Description: Perform operations on Newick trees + EDAM operation: + - Phylogenetic tree generation + - Phylogenetic tree analysis + - Phylogenetic tree reconstruction + EDAM operation (no superclasses): [] + EDAM topic: + - Phylogeny + - Genomics + - Computer science + EDAM topic (no superclasses): + - Phylogeny + - Genomics + - Computer science + Galaxy tool ids: + - newick_display + Galaxy wrapper id: newick_utils + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils + Galaxy wrapper source: https://github.com/tjunier/newick_utils + Galaxy wrapper version: 1.6+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 33637 + No. of tool users (5 years) (usegalaxy.org): 16257 + No. of tool users (5 years) (usegalaxy.org.au): 7582 + No. of tool users (5 years) - all main servers: 57476 + No. of tool users (all time) (usegalaxy.eu): 34195 + No. of tool users (all time) (usegalaxy.org): 16257 + No. of tool users (all time) (usegalaxy.org.au): 7582 + No. of tool users (all time) - all main servers: 58034 + Source: http://cegg.unige.ch/newick_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1113 + Tool usage (5 years) (usegalaxy.org): 1816 + Tool usage (5 years) (usegalaxy.org.au): 899 + Tool usage (5 years) - all main servers: 3828 + Tool usage (all time) (usegalaxy.eu): 1172 + Tool usage (all time) (usegalaxy.org): 1816 + Tool usage (all time) (usegalaxy.org.au): 899 + Tool usage (all time) - all main servers: 3887 + ToolShed categories: + - Visualization + - Metagenomics + ToolShed id: newick_utils + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: The Newick Utilities are a set of command-line tools for processing + phylogenetic trees. They can process arbitrarily large amounts of data and do + not require user interaction, which makes them suitable for automating phylogeny + processing tasks. + bio.tool id: newick_utilities + bio.tool ids: + - newick_utilities + bio.tool name: Newick Utilities +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: nextalign + Conda version: 2.14.0 + Date of first commit of the suite: '2021-04-26' + Description: Identify differences between your sequences and a reference sequence + used by Nextstrain + EDAM operation: + - Methylation analysis + - Variant calling + EDAM operation (no superclasses): + - Methylation analysis + - Variant calling + EDAM topic: + - Genomics + - Sequence analysis + - Cladistics + EDAM topic (no superclasses): + - Genomics + - Cladistics + Galaxy tool ids: + - nextalign + - nextclade + Galaxy wrapper id: nextclade + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade + Galaxy wrapper version: 2.7.0 + No. of tool users (5 years) (usegalaxy.eu): 4411 + No. of tool users (5 years) (usegalaxy.org): 9708 + No. of tool users (5 years) (usegalaxy.org.au): 2099 + No. of tool users (5 years) - all main servers: 16218 + No. of tool users (all time) (usegalaxy.eu): 4411 + No. of tool users (all time) (usegalaxy.org): 9708 + No. of tool users (all time) (usegalaxy.org.au): 2099 + No. of tool users (all time) - all main servers: 16218 + Source: https://github.com/nextstrain/nextclade + Status: To update + Tool usage (5 years) (usegalaxy.eu): 396 + Tool usage (5 years) (usegalaxy.org): 279 + Tool usage (5 years) (usegalaxy.org.au): 212 + Tool usage (5 years) - all main servers: 887 + Tool usage (all time) (usegalaxy.eu): 396 + Tool usage (all time) (usegalaxy.org): 279 + Tool usage (all time) (usegalaxy.org.au): 212 + Tool usage (all time) - all main servers: 887 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Nextclade is an open-source project for viral genome alignment, + mutation calling, clade assignment, quality checks and phylogenetic placement. + bio.tool id: nextclade + bio.tool ids: + - nextclade + bio.tool name: Nextclade +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ngmlr + Conda version: 0.2.7 + Date of first commit of the suite: '2020-10-27' + Description: CoNvex Gap-cost alignMents for Long Reads + EDAM operation: + - DNA mapping + - Sequence alignment + - Genetic variation analysis + EDAM operation (no superclasses): + - DNA mapping + - Sequence alignment + - Genetic variation analysis + EDAM topic: + - Sequencing + - Mapping + - DNA structural variation + EDAM topic (no superclasses): + - Sequencing + - Mapping + Galaxy tool ids: + - ngmlr + Galaxy wrapper id: ngmlr + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr + Galaxy wrapper version: 0.2.7 + No. of tool users (5 years) (usegalaxy.eu): 1403 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1403 + No. of tool users (all time) (usegalaxy.eu): 1403 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1403 + Source: https://github.com/philres/ngmlr + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 49 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 49 + Tool usage (all time) (usegalaxy.eu): 49 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 49 + ToolShed categories: + - Next Gen Mappers + ToolShed id: ngmlr + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: An algorithm to map third generation long-read sequencing + data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads + that span structural variation. + bio.tool id: ngmlr + bio.tool ids: + - ngmlr + bio.tool name: NGMLR +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: ngsutils + Conda version: 0.5.9 + Date of first commit of the suite: '2015-11-10' + Description: NGSUtils is a suite of software tools for working with next-generation + sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School + of Medicine) starting working withnext-generation sequencing data. We initially + started doing custom coding for each project in a one-off manner.It quickly became + apparent that this was an inefficient manner to work, so we started assembling + smallerutilities that could be adapted into larger, more complicated, workflows. + We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing + data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted + resequencing (Agilent exome capture and PCR targeting).These tools are also used + heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ + programs, mainly written in Python.These are separated into modules based on the + type of file that is to be analyzed. + EDAM operation: + - Read pre-processing + - Sequencing quality control + - Variant calling + - Formatting + - Sequence contamination filtering + EDAM operation (no superclasses): + - Read pre-processing + - Variant calling + - Formatting + - Sequence contamination filtering + EDAM topic: + - Genomics + - Transcriptomics + EDAM topic (no superclasses): + - Transcriptomics + Galaxy tool ids: + - ngsutils_bam_filter + Galaxy wrapper id: ngsutils + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 24611 + No. of tool users (5 years) (usegalaxy.org): 15523 + No. of tool users (5 years) (usegalaxy.org.au): 7751 + No. of tool users (5 years) - all main servers: 47885 + No. of tool users (all time) (usegalaxy.eu): 29662 + No. of tool users (all time) (usegalaxy.org): 21395 + No. of tool users (all time) (usegalaxy.org.au): 8972 + No. of tool users (all time) - all main servers: 60029 + Source: https://github.com/ngsutils/ngsutils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 633 + Tool usage (5 years) (usegalaxy.org): 740 + Tool usage (5 years) (usegalaxy.org.au): 125 + Tool usage (5 years) - all main servers: 1498 + Tool usage (all time) (usegalaxy.eu): 716 + Tool usage (all time) (usegalaxy.org): 1128 + Tool usage (all time) (usegalaxy.org.au): 145 + Tool usage (all time) - all main servers: 1989 + ToolShed categories: + - SAM + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: NGSUtils is a suite of software tools for working with next-generation + sequencing datasets + bio.tool id: ngsutils + bio.tool ids: + - ngsutils + bio.tool name: NGSUtils +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: nonpareil + Conda version: 3.5.5 + Date of first commit of the suite: '2017-11-03' + Description: Estimate average coverage in metagenomic datasets + EDAM operation: + - Operation + EDAM operation (no superclasses): + - Operation + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - nonpareil + Galaxy wrapper id: nonpareil + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil + Galaxy wrapper version: 3.1.1 + No. of tool users (5 years) (usegalaxy.eu): 107 + No. of tool users (5 years) (usegalaxy.org): 148 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 255 + No. of tool users (all time) (usegalaxy.eu): 143 + No. of tool users (all time) (usegalaxy.org): 148 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 291 + Source: http://nonpareil.readthedocs.io + Status: To update + Tool usage (5 years) (usegalaxy.eu): 13 + Tool usage (5 years) (usegalaxy.org): 20 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 33 + Tool usage (all time) (usegalaxy.eu): 15 + Tool usage (all time) (usegalaxy.org): 20 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 35 + ToolShed categories: + - Metagenomics + ToolShed id: nonpareil + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Estimate metagenomic coverage and sequence diversity + bio.tool id: nonpareil + bio.tool ids: + - nonpareil + bio.tool name: nonpareil +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: novoplasty + Conda version: 4.3.5 + Date of first commit of the suite: '2020-05-18' + Description: NOVOPlasty is a de novo assembler and heteroplasmy/variance caller + for short circular genomes. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - novoplasty + Galaxy wrapper id: novoplasty + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty + Galaxy wrapper version: 4.3.1 + No. of tool users (5 years) (usegalaxy.eu): 7780 + No. of tool users (5 years) (usegalaxy.org): 1 + No. of tool users (5 years) (usegalaxy.org.au): 2323 + No. of tool users (5 years) - all main servers: 10104 + No. of tool users (all time) (usegalaxy.eu): 7780 + No. of tool users (all time) (usegalaxy.org): 1 + No. of tool users (all time) (usegalaxy.org.au): 2323 + No. of tool users (all time) - all main servers: 10104 + Source: https://github.com/ndierckx/NOVOPlasty + Status: To update + Tool usage (5 years) (usegalaxy.eu): 337 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 99 + Tool usage (5 years) - all main servers: 437 + Tool usage (all time) (usegalaxy.eu): 337 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 99 + Tool usage (all time) - all main servers: 437 + ToolShed categories: + - Assembly + ToolShed id: novoplasty + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: nudup + Conda version: 2.3.3 + Date of first commit of the suite: '2016-11-18' + Description: Marks/removes PCR introduced duplicate molecules based on the molecular + tagging technology used in NuGEN products. + EDAM operation: + - Duplication detection + EDAM operation (no superclasses): + - Duplication detection + EDAM topic: + - Sequencing + EDAM topic (no superclasses): + - Sequencing + Galaxy tool ids: + - nugen_nudup + Galaxy wrapper id: nugen_nudup + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup + Galaxy wrapper version: 2.3.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/tecangenomics/nudup + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - SAM + - Metagenomics + - Sequence Analysis + - Transcriptomics + ToolShed id: nugen_nudup + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: Marks/removes duplicate molecules based on the molecular tagging + technology used in Tecan products. + bio.tool id: nudup + bio.tool ids: + - nudup + bio.tool name: NuDup +- Available on UseGalaxy.eu: 10 + Available on UseGalaxy.fr: 10 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 10 + Conda id: obitools + Conda version: 1.2.13 + Date of first commit of the suite: '2017-03-23' + Description: OBITools is a set of programs developed to simplify the manipulation + of sequence files + EDAM operation: + - Sequence analysis + - Sequence analysis + EDAM operation (no superclasses): + - Sequence analysis + - Sequence analysis + EDAM topic: + - Sequence analysis + - DNA + - Sequencing + EDAM topic (no superclasses): + - Sequence analysis + - DNA + - Sequencing + Galaxy tool ids: + - obi_illumina_pairend + - obi_ngsfilter + - obi_annotate + - obi_clean + - obi_convert + - obi_grep + - obi_sort + - obi_stat + - obi_tab + - obi_uniq + Galaxy wrapper id: obitools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools + Galaxy wrapper version: 1.2.13 + No. of tool users (5 years) (usegalaxy.eu): 37598 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 3862 + No. of tool users (5 years) - all main servers: 41460 + No. of tool users (all time) (usegalaxy.eu): 37598 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 3862 + No. of tool users (all time) - all main servers: 41460 + Source: http://metabarcoding.org/obitools + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1277 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 280 + Tool usage (5 years) - all main servers: 1557 + Tool usage (all time) (usegalaxy.eu): 1277 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 280 + Tool usage (all time) - all main servers: 1557 + ToolShed categories: + - Sequence Analysis + ToolShed id: obitools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 10 + Tools available on UseGalaxy.eu: 10 + Tools available on UseGalaxy.fr: 10 + Tools available on UseGalaxy.no: 10 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 10 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 10 + UseGalaxy.eu: 10 + UseGalaxy.fr: 10 + UseGalaxy.no: 10 + UseGalaxy.or: 10 + biii: null + bio.tool description: Set of python programs developed to simplify the manipulation + of sequence files. They were mainly designed to help us for analyzing Next Generation + Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. + bio.tool id: obitools + bio.tool ids: + - obitools + bio.tool name: OBITools +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: ococo + Conda version: 0.1.2.7 + Date of first commit of the suite: '2017-12-07' + Description: Variant detection of SNVs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ococo + Galaxy wrapper id: ococo + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo + Galaxy wrapper version: 0.1.2.6 + No. of tool users (5 years) (usegalaxy.eu): 1850 + No. of tool users (5 years) (usegalaxy.org): 1370 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3220 + No. of tool users (all time) (usegalaxy.eu): 1963 + No. of tool users (all time) (usegalaxy.org): 1370 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3333 + Source: https://github.com/karel-brinda/ococo + Status: To update + Tool usage (5 years) (usegalaxy.eu): 79 + Tool usage (5 years) (usegalaxy.org): 194 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 273 + Tool usage (all time) (usegalaxy.eu): 93 + Tool usage (all time) (usegalaxy.org): 194 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 287 + ToolShed categories: + - Variant Analysis + ToolShed id: ococo + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: odgi + Conda version: 0.9.0 + Date of first commit of the suite: '2020-04-06' + Description: Representing large genomic variation graphs with minimal memory overhead + requires a careful encoding of the graph entities. odgi follows the dynamic GBWT + in developing a byte-packed version of the graph and paths through it. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - odgi_build + - odgi_viz + Galaxy wrapper id: odgi + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ + Galaxy wrapper version: '0.3' + No. of tool users (5 years) (usegalaxy.eu): 26 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 26 + No. of tool users (all time) (usegalaxy.eu): 26 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 26 + Source: https://github.com/vgteam/odgi + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-11-15' + Description: Proteome quality assessment software + EDAM operation: + - Sequence assembly validation + - Differential protein expression profiling + EDAM operation (no superclasses): + - Sequence assembly validation + - Differential protein expression profiling + EDAM topic: + - Proteomics + - Sequence analysis + - Statistics and probability + EDAM topic (no superclasses): + - Proteomics + - Sequence analysis + - Statistics and probability + Galaxy tool ids: + - omark + Galaxy wrapper id: omark + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ + Galaxy wrapper version: 0.3.0 + No. of tool users (5 years) (usegalaxy.eu): 158 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 158 + No. of tool users (all time) (usegalaxy.eu): 158 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 158 + Source: https://github.com/DessimozLab/OMArk + Status: To update + Tool usage (5 years) (usegalaxy.eu): 12 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 12 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - Sequence Analysis + ToolShed id: omark + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Proteome quality assessment software + bio.tool id: omark + bio.tool ids: + - omark + bio.tool name: OMArk +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ont-fast5-api + Conda version: 4.1.3 + Date of first commit of the suite: '2020-06-08' + Description: ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore + FAST5 file format. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ont_fast5_api_compress_fast5 + - ont_fast5_api_fast5_subset + - ont_fast5_api_multi_to_single_fast5 + - ont_fast5_api_single_to_multi_fast5 + Galaxy wrapper id: ont_fast5_api + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api + Galaxy wrapper version: 3.1.3 + No. of tool users (5 years) (usegalaxy.eu): 3051 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3051 + No. of tool users (all time) (usegalaxy.eu): 3051 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3051 + Source: https://github.com/nanoporetech/ont_fast5_api/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 87 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 87 + Tool usage (all time) (usegalaxy.eu): 87 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 87 + ToolShed categories: + - Nanopore + ToolShed id: ont_fast5_api + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 4 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 4 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 4 + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 1 + UseGalaxy.no: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 17 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-onto-perl + Conda version: '1.45' + Date of first commit of the suite: '2017-11-04' + Description: ONTO-Toolkit is a collection of tools for managing ontologies. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - onto_tk_get_ancestor_terms + - onto_tk_get_child_terms + - onto_tk_get_descendent_terms + - onto_tk_get_parent_terms + - onto_tk_get_parent_terms_by_relationship_type + - onto_tk_get_relationship_id_vs_relationship_def + - onto_tk_get_relationship_id_vs_relationship_name + - onto_tk_get_relationship_id_vs_relationship_namespace + - onto_tk_get_relationship_types + - onto_tk_get_root_terms + - onto_tk_get_subontology_from + - onto_tk_term_id_vs_term_def + - onto_tk_term_id_vs_term_name + - onto_tk_get_term_synonyms + - onto_tk_get_terms + - onto_tk_get_terms_by_relationship_type + - onto_tk_obo2owl + - onto_tk_obo2rdf + - onto_tk_term_id_vs_term_def + Galaxy wrapper id: onto_toolkit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit + Galaxy wrapper version: '1.45' + No. of tool users (5 years) (usegalaxy.eu): 582 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 582 + No. of tool users (all time) (usegalaxy.eu): 663 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 663 + Source: http://search.cpan.org/~easr/ONTO-PERL-1.45/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 68 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 68 + Tool usage (all time) (usegalaxy.eu): 69 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 69 + ToolShed categories: + - Ontology Manipulation + ToolShed id: onto_toolkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 17 + Tools available on UseGalaxy.eu: 17 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 17 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 17 + UseGalaxy.eu: 17 + UseGalaxy.no: 17 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: doebase + Conda version: null + Date of first commit of the suite: '2022-10-27' + Description: Optimal Design Of Experiment + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - optdoe + Galaxy wrapper id: optdoe + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe + Galaxy wrapper version: v2.0.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/pablocarb/doebase + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: optdoe + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: optitype + Conda version: 1.3.5 + Date of first commit of the suite: '2021-02-17' + Description: Precision HLA typing from NGS data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - optitype + Galaxy wrapper id: optitype + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 + Galaxy wrapper version: 1.3.5 + No. of tool users (5 years) (usegalaxy.eu): 500 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 500 + No. of tool users (all time) (usegalaxy.eu): 500 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 500 + Source: https://github.com/FRED-2/OptiType + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 45 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 45 + Tool usage (all time) (usegalaxy.eu): 45 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 45 + ToolShed categories: + - Sequence Analysis + ToolShed id: optitype + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: orfipy + Conda version: 0.0.4 + Date of first commit of the suite: '2022-04-07' + Description: Galaxy wrapper for ORFIPY + EDAM operation: + - Coding region prediction + - Database search + - Transcriptome assembly + - De-novo assembly + EDAM operation (no superclasses): + - Coding region prediction + - Database search + - Transcriptome assembly + - De-novo assembly + EDAM topic: + - Computer science + - RNA-Seq + - Transcriptomics + - Small molecules + EDAM topic (no superclasses): + - Computer science + - RNA-Seq + - Transcriptomics + - Small molecules + Galaxy tool ids: + - orfipy + Galaxy wrapper id: orfipy + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy + Galaxy wrapper version: 0.0.4 + No. of tool users (5 years) (usegalaxy.eu): 897 + No. of tool users (5 years) (usegalaxy.org): 1792 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2689 + No. of tool users (all time) (usegalaxy.eu): 897 + No. of tool users (all time) (usegalaxy.org): 1792 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2689 + Source: https://github.com/urmi-21/orfipy + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 99 + Tool usage (5 years) (usegalaxy.org): 239 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 338 + Tool usage (all time) (usegalaxy.eu): 99 + Tool usage (all time) (usegalaxy.org): 239 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 338 + ToolShed categories: + - Sequence Analysis + ToolShed id: orfipy + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A fast and flexible tool for extracting ORFs.orfipy is a tool + written in python/cython to extract ORFs in extremely an fast and flexible manner. + Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, + orfipy provides the most options to fine tune ORF searches. orfipy uses multiple + CPU cores and is particularly faster for data containing multiple smaller fasta + sequences such as de-novo transcriptome assemblies. Please read the preprint here. + bio.tool id: orfipy + bio.tool ids: + - orfipy + bio.tool name: orfipy +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: orthofinder + Conda version: 3.0.1b1 + Date of first commit of the suite: '2017-08-30' + Description: Accurate inference of orthologous gene groups made easy + EDAM operation: + - Genome comparison + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree analysis + - Genome alignment + EDAM operation (no superclasses): + - Genome comparison + - Genome alignment + EDAM topic: + - Phylogenetics + - Phylogenomics + - Bioinformatics + - Comparative genomics + - Sequence analysis + EDAM topic (no superclasses): + - Phylogenetics + - Phylogenomics + - Bioinformatics + - Comparative genomics + Galaxy tool ids: + - orthofinder_onlygroups + Galaxy wrapper id: orthofinder + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder + Galaxy wrapper version: 2.5.5 + No. of tool users (5 years) (usegalaxy.eu): 2018 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 438 + No. of tool users (5 years) - all main servers: 2456 + No. of tool users (all time) (usegalaxy.eu): 2018 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 438 + No. of tool users (all time) - all main servers: 2456 + Source: https://github.com/davidemms/OrthoFinder + Status: To update + Tool usage (5 years) (usegalaxy.eu): 419 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 58 + Tool usage (5 years) - all main servers: 477 + Tool usage (all time) (usegalaxy.eu): 419 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 58 + Tool usage (all time) - all main servers: 477 + ToolShed categories: + - Phylogenetics + - Sequence Analysis + ToolShed id: orthofinder + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: OrthoFinder is a fast, accurate and comprehensive platform + for comparative genomics. It finds orthogroups and orthologs, infers rooted gene + trees for all orthogroups and identifies all of the gene duplcation events in + those gene trees. It also infers a rooted species tree for the species being analysed + and maps the gene duplication events from the gene trees to branches in the species + tree. OrthoFinder also provides comprehensive statistics for comparative genomic + analyses. + bio.tool id: OrthoFinder + bio.tool ids: + - OrthoFinder + bio.tool name: OrthoFinder +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2022-01-04' + Description: Tool to make cached genome annotation data available as a list of datasets + collection + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - packaged_annotation_loader + Galaxy wrapper id: packaged_annotation_loader + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Data Source + ToolShed id: packaged_annotation_loader + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pacu_snp + Conda version: 0.0.5 + Date of first commit of the suite: '2024-08-13' + Description: PACU is a workflow for whole genome sequencing based phylogeny of Illumina + and ONT R9/R10 data. + EDAM operation: + - Clustering + EDAM operation (no superclasses): + - Clustering + EDAM topic: + - Phylogenetics + - Sequence analysis + EDAM topic (no superclasses): + - Phylogenetics + Galaxy tool ids: + - pacu_map + - pacu_snp + Galaxy wrapper id: pacu + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu + Galaxy wrapper version: 0.0.5 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/BioinformaticsPlatformWIV-ISP/PACU + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + - Phylogenetics + ToolShed id: pacu + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + biii: null + bio.tool description: PACU is a workflow for whole genome sequencing based phylogeny + of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant + Calling Utility and is named after an omnivorous fish (that eats both Illumina + and ONT reads). + bio.tool id: pacu + bio.tool ids: + - pacu + bio.tool name: PACU +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 0 + Conda id: pairtools + Conda version: 1.1.0 + Date of first commit of the suite: '2024-03-26' + Description: Flexible tools for Hi-C data processing + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pairtools_dedup + - pairtools_parse + - pairtools_sort + - pairtools_split + - pairtools_stats + Galaxy wrapper id: pairtools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools + Galaxy wrapper source: https://github.com/open2c/pairtools + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 196 + No. of tool users (5 years) (usegalaxy.org): 19 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 215 + No. of tool users (all time) (usegalaxy.eu): 196 + No. of tool users (all time) (usegalaxy.org): 19 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 215 + Source: https://pairtools.readthedocs.io + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 14 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 30 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 14 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 30 + ToolShed categories: + - Sequence Analysis + ToolShed id: pairtools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pangolin + Conda version: '4.3' + Date of first commit of the suite: '2021-04-25' + Description: Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages + under the Pango nomenclature system. + EDAM operation: + - Tree-based sequence alignment + - Variant classification + EDAM operation (no superclasses): + - Tree-based sequence alignment + - Variant classification + EDAM topic: + - Virology + EDAM topic (no superclasses): + - Virology + Galaxy tool ids: + - pangolin + Galaxy wrapper id: pangolin + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin + Galaxy wrapper version: '4.3' + No. of tool users (5 years) (usegalaxy.eu): 7457 + No. of tool users (5 years) (usegalaxy.org): 8518 + No. of tool users (5 years) (usegalaxy.org.au): 2760 + No. of tool users (5 years) - all main servers: 18735 + No. of tool users (all time) (usegalaxy.eu): 7457 + No. of tool users (all time) (usegalaxy.org): 8518 + No. of tool users (all time) (usegalaxy.org.au): 2760 + No. of tool users (all time) - all main servers: 18735 + Source: https://github.com/cov-lineages/pangolin + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 508 + Tool usage (5 years) (usegalaxy.org): 377 + Tool usage (5 years) (usegalaxy.org.au): 259 + Tool usage (5 years) - all main servers: 1144 + Tool usage (all time) (usegalaxy.eu): 508 + Tool usage (all time) (usegalaxy.org): 377 + Tool usage (all time) (usegalaxy.org.au): 259 + Tool usage (all time) - all main servers: 1144 + ToolShed categories: + - Sequence Analysis + ToolShed id: pangolin + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Phylogenetic Assignment of Named Global Outbreak LINeages + - software package for assigning SARS-CoV-2 genome sequences to global lineages + bio.tool id: pangolin_cov-lineages + bio.tool ids: + - pangolin_cov-lineages + bio.tool name: pangolin +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: parse_mito_blast + Conda version: 1.0.2 + Date of first commit of the suite: '2022-05-12' + Description: Filtering blast out from querying assembly against mitochondrial database. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - parse_mito_blast + Galaxy wrapper id: parse_mito_blast + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 203 + No. of tool users (5 years) (usegalaxy.org): 288 + No. of tool users (5 years) (usegalaxy.org.au): 110 + No. of tool users (5 years) - all main servers: 601 + No. of tool users (all time) (usegalaxy.eu): 203 + No. of tool users (all time) (usegalaxy.org): 288 + No. of tool users (all time) (usegalaxy.org.au): 110 + No. of tool users (all time) - all main servers: 601 + Source: https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 65 + Tool usage (5 years) (usegalaxy.org): 62 + Tool usage (5 years) (usegalaxy.org.au): 20 + Tool usage (5 years) - all main servers: 147 + Tool usage (all time) (usegalaxy.eu): 65 + Tool usage (all time) (usegalaxy.org): 62 + Tool usage (all time) (usegalaxy.org.au): 20 + Tool usage (all time) - all main servers: 147 + ToolShed categories: + - Sequence Analysis + ToolShed id: parse_mito_blast + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-pathview + Conda version: 1.42.0 + Date of first commit of the suite: '2019-08-26' + Description: Pathview is a tool set for pathway based data integration and visualization. + EDAM operation: + - Pathway or network analysis + - Pathway or network visualisation + EDAM operation (no superclasses): + - Pathway or network analysis + - Pathway or network visualisation + EDAM topic: + - Molecular interactions, pathways and networks + - Systems biology + - Data visualisation + EDAM topic (no superclasses): + - Molecular interactions, pathways and networks + - Systems biology + - Data visualisation + Galaxy tool ids: + - pathview + Galaxy wrapper id: pathview + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview + Galaxy wrapper version: 1.34.0 + No. of tool users (5 years) (usegalaxy.eu): 6204 + No. of tool users (5 years) (usegalaxy.org): 6667 + No. of tool users (5 years) (usegalaxy.org.au): 1160 + No. of tool users (5 years) - all main servers: 14031 + No. of tool users (all time) (usegalaxy.eu): 6211 + No. of tool users (all time) (usegalaxy.org): 6667 + No. of tool users (all time) (usegalaxy.org.au): 1160 + No. of tool users (all time) - all main servers: 14038 + Source: https://bioconductor.org/packages/release/bioc/html/pathview.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1261 + Tool usage (5 years) (usegalaxy.org): 1143 + Tool usage (5 years) (usegalaxy.org.au): 189 + Tool usage (5 years) - all main servers: 2593 + Tool usage (all time) (usegalaxy.eu): 1261 + Tool usage (all time) (usegalaxy.org): 1143 + Tool usage (all time) (usegalaxy.org.au): 189 + Tool usage (all time) - all main servers: 2593 + ToolShed categories: + - Statistics + - RNA + - Micro-array Analysis + ToolShed id: pathview + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Tool set for pathway based data integration and visualization + that maps and renders a wide variety of biological data on relevant pathway graphs. + It downloads the pathway graph data, parses the data file, maps user data to the + pathway, and render pathway graph with the mapped data. In addition, it integrates + with pathway and gene set (enrichment) analysis tools for large-scale and fully + automated analysis. + bio.tool id: pathview + bio.tool ids: + - pathview + bio.tool name: pathview +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pbgcpp + Conda version: 2.0.2 + Date of first commit of the suite: '2022-03-14' + Description: Compute genomic consensus and call variants using PacBio reads mapped + to a reference + EDAM operation: + - Variant calling + EDAM operation (no superclasses): + - Variant calling + EDAM topic: + - Mapping + EDAM topic (no superclasses): + - Mapping + Galaxy tool ids: + - pbgcpp + Galaxy wrapper id: pbgcpp + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp + Galaxy wrapper version: 2.0.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/PacificBiosciences/gcpp + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: pbgcpp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: The GenomicConsensus package provides the variantCaller tool, + which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads + to get consensus and variant calls. + bio.tool id: genomicconsensus + bio.tool ids: + - genomicconsensus + bio.tool name: GenomicConsensus +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pbmm2 + Conda version: 1.14.99 + Date of first commit of the suite: '2022-03-23' + Description: A minimap2 SMRT wrapper for PacBio data. + EDAM operation: + - Pairwise sequence alignment + - Sorting + EDAM operation (no superclasses): + - Pairwise sequence alignment + - Sorting + EDAM topic: + - Mapping + EDAM topic (no superclasses): + - Mapping + Galaxy tool ids: + - pbmm2 + Galaxy wrapper id: pbmm2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 + Galaxy wrapper version: 1.14.99 + No. of tool users (5 years) (usegalaxy.eu): 70 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 70 + No. of tool users (all time) (usegalaxy.eu): 70 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 70 + Source: https://github.com/PacificBiosciences/pbmm2 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 17 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 17 + ToolShed categories: + - Next Gen Mappers + ToolShed id: pbmm2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose + is to support native PacBio in- and output, provide sets of recommended parameters, + generate sorted output on-the-fly, and postprocess alignments. Sorted output can + be used directly for polishing using GenomicConsensus, if BAM has been used as + input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, + number of mapped bases, and especially runtime. pbmm2 is the official replacement + for BLASR. + bio.tool id: pbmm2 + bio.tool ids: + - pbmm2 + bio.tool name: pbmm2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: pbtk + Conda version: 3.1.1 + Date of first commit of the suite: '2024-03-11' + Description: Convert PacBio Bam File to fasta or fastq file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bam2fastx + Galaxy wrapper id: pbtk + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk + Galaxy wrapper version: 3.1.1 + No. of tool users (5 years) (usegalaxy.eu): 58 + No. of tool users (5 years) (usegalaxy.org): 109 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 167 + No. of tool users (all time) (usegalaxy.eu): 58 + No. of tool users (all time) (usegalaxy.org): 109 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 167 + Source: https://github.com/PacificBiosciences/pbtk + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 22 + Tool usage (5 years) (usegalaxy.org): 19 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 41 + Tool usage (all time) (usegalaxy.eu): 22 + Tool usage (all time) (usegalaxy.org): 19 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 41 + ToolShed categories: + - Convert Formats + - Fasta Manipulation + - Fastq Manipulation + ToolShed id: bam2fastx + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: openjdk + Conda version: null + Date of first commit of the suite: '2016-06-16' + Description: Contains a tool that produces an insert size histogram for a paired-end + BAM file. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pe_histogram + Galaxy wrapper id: pe_histogram + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 5505 + No. of tool users (5 years) (usegalaxy.org): 7932 + No. of tool users (5 years) (usegalaxy.org.au): 736 + No. of tool users (5 years) - all main servers: 14173 + No. of tool users (all time) (usegalaxy.eu): 5505 + No. of tool users (all time) (usegalaxy.org): 8582 + No. of tool users (all time) (usegalaxy.org.au): 736 + No. of tool users (all time) - all main servers: 14823 + Source: https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram + Status: To update + Tool usage (5 years) (usegalaxy.eu): 510 + Tool usage (5 years) (usegalaxy.org): 811 + Tool usage (5 years) (usegalaxy.org.au): 119 + Tool usage (5 years) - all main servers: 1440 + Tool usage (all time) (usegalaxy.eu): 510 + Tool usage (all time) (usegalaxy.org): 909 + Tool usage (all time) (usegalaxy.org.au): 119 + Tool usage (all time) - all main servers: 1538 + ToolShed categories: + - Graphics + ToolShed id: pe_histogram + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2024-02-25' + Description: Peakzilla identifies sites of enrichment and transcription factor binding + sites from ChIP-seq and ChIP-exo experiments. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - peakzilla + Galaxy wrapper id: peakzilla + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 18 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 18 + No. of tool users (all time) (usegalaxy.eu): 18 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 18 + Source: https://github.com/steinmann/peakzilla + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - ChIP-seq + ToolShed id: peakzilla + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pear + Conda version: 0.9.6 + Date of first commit of the suite: '2015-02-11' + Description: PEAR evaluates all possible paired-end read overlaps + EDAM operation: + - Sequence merging + EDAM operation (no superclasses): + - Sequence merging + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - iuc_pear + Galaxy wrapper id: pear + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear + Galaxy wrapper version: 0.9.6 + No. of tool users (5 years) (usegalaxy.eu): 6269 + No. of tool users (5 years) (usegalaxy.org): 5530 + No. of tool users (5 years) (usegalaxy.org.au): 5647 + No. of tool users (5 years) - all main servers: 17446 + No. of tool users (all time) (usegalaxy.eu): 6866 + No. of tool users (all time) (usegalaxy.org): 20068 + No. of tool users (all time) (usegalaxy.org.au): 8471 + No. of tool users (all time) - all main servers: 35405 + Source: https://cme.h-its.org/exelixis/web/software/pear/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 260 + Tool usage (5 years) (usegalaxy.org): 467 + Tool usage (5 years) (usegalaxy.org.au): 198 + Tool usage (5 years) - all main servers: 925 + Tool usage (all time) (usegalaxy.eu): 292 + Tool usage (all time) (usegalaxy.org): 1664 + Tool usage (all time) (usegalaxy.org.au): 300 + Tool usage (all time) - all main servers: 2256 + ToolShed categories: + - Fastq Manipulation + ToolShed id: pear + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Paired-end read merger. PEAR evaluates all possible paired-end + read overlaps without requiring the target fragment size as input. In addition, + it implements a statistical test for minimizing false-positive results. + bio.tool id: pear + bio.tool ids: + - pear + bio.tool name: PEAR +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: "\n pharokka\n " + Conda version: null + Date of first commit of the suite: '2023-02-14' + Description: rapid standardised annotation tool for bacteriophage genomes and metagenomes + EDAM operation: + - Genome annotation + - Antimicrobial resistance prediction + - tRNA gene prediction + - Formatting + - Sequence assembly + EDAM operation (no superclasses): + - Genome annotation + - Antimicrobial resistance prediction + - tRNA gene prediction + - Formatting + - Sequence assembly + EDAM topic: + - Metagenomics + - Sequence sites, features and motifs + - Workflows + - Functional, regulatory and non-coding RNA + EDAM topic (no superclasses): + - Metagenomics + - Sequence sites, features and motifs + - Workflows + - Functional, regulatory and non-coding RNA + Galaxy tool ids: + - pharokka + Galaxy wrapper id: pharokka + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka + Galaxy wrapper version: 1.3.2 + No. of tool users (5 years) (usegalaxy.eu): 5462 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 309 + No. of tool users (5 years) - all main servers: 5771 + No. of tool users (all time) (usegalaxy.eu): 5462 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 309 + No. of tool users (all time) - all main servers: 5771 + Source: https://github.com/gbouras13/pharokka + Status: To update + Tool usage (5 years) (usegalaxy.eu): 334 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 52 + Tool usage (5 years) - all main servers: 386 + Tool usage (all time) (usegalaxy.eu): 334 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 52 + Tool usage (all time) - all main servers: 386 + ToolShed categories: + - Genome annotation + ToolShed id: pharokka + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Pharokka is a rapid standardised annotation tool for bacteriophage + genomes and metagenomes. + bio.tool id: pharokka + bio.tool ids: + - pharokka + bio.tool name: Pharokka +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-phyloseq + Conda version: 1.46.0 + Date of first commit of the suite: '2022-03-03' + Description: Handling and analysis of high-throughput microbiome census data + EDAM operation: + - Deposition + - Analysis + - Visualisation + EDAM operation (no superclasses): + - Deposition + - Analysis + - Visualisation + EDAM topic: + - Microbiology + - Sequence analysis + - Metagenomics + EDAM topic (no superclasses): + - Microbiology + - Sequence analysis + - Metagenomics + Galaxy tool ids: + - phyloseq_from_biom + - phyloseq_from_dada2 + - phyloseq_plot_ordination + - phyloseq_plot_richness + Galaxy wrapper id: phyloseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq + Galaxy wrapper version: 1.46.0 + No. of tool users (5 years) (usegalaxy.eu): 1199 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 6 + No. of tool users (5 years) - all main servers: 1205 + No. of tool users (all time) (usegalaxy.eu): 1199 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 6 + No. of tool users (all time) - all main servers: 1205 + Source: https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 193 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 194 + Tool usage (all time) (usegalaxy.eu): 193 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 194 + ToolShed categories: + - Metagenomics + ToolShed id: phyloseq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 4 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 4 + UseGalaxy.fr: 4 + UseGalaxy.no: 3 + UseGalaxy.or: 1 + biii: null + bio.tool description: Provides a set of classes and tools to facilitate the import, + storage, analysis, and graphical display of microbiome census data. + bio.tool id: phyloseq + bio.tool ids: + - phyloseq + bio.tool name: phyloseq +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: phyml + Conda version: 3.3.20220408 + Date of first commit of the suite: '2019-05-27' + Description: PhyML is a phylogeny software based on the maximum-likelihood principle. + EDAM operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + EDAM operation (no superclasses): [] + EDAM topic: + - Phylogenetics + - Bioinformatics + - Phylogenetics + EDAM topic (no superclasses): + - Phylogenetics + - Bioinformatics + - Phylogenetics + Galaxy tool ids: + - phyml + Galaxy wrapper id: phyml + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml + Galaxy wrapper version: 3.3.20220408 + No. of tool users (5 years) (usegalaxy.eu): 1975 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 553 + No. of tool users (5 years) - all main servers: 2528 + No. of tool users (all time) (usegalaxy.eu): 2034 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 564 + No. of tool users (all time) - all main servers: 2598 + Source: http://www.atgc-montpellier.fr/phyml/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 246 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 140 + Tool usage (5 years) - all main servers: 386 + Tool usage (all time) (usegalaxy.eu): 258 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 144 + Tool usage (all time) - all main servers: 402 + ToolShed categories: + - Phylogenetics + ToolShed id: phyml + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Phylogenetic estimation software using Maximum Likelihood + bio.tool id: phyml + bio.tool ids: + - phyml + bio.tool name: PhyML +- Available on UseGalaxy.eu: 31 + Available on UseGalaxy.fr: 31 + Available on UseGalaxy.org (Main): 31 + Available on UseGalaxy.org.au: 31 + Conda id: picard + Conda version: 3.3.0 + Date of first commit of the suite: '2019-05-30' + Description: Picard SAM/BAM manipulation tools. + EDAM operation: + - Formatting + EDAM operation (no superclasses): + - Formatting + EDAM topic: + - Sequencing + EDAM topic (no superclasses): + - Sequencing + Galaxy tool ids: + - picard_AddCommentsToBam + - picard_AddOrReplaceReadGroups + - picard_BedToIntervalList + - picard_CleanSam + - picard_CASM + - picard_CollectBaseDistributionByCycle + - picard_CollectGcBiasMetrics + - picard_CollectHsMetrics + - picard_CollectInsertSizeMetrics + - picard_CollectRnaSeqMetrics + - picard_artifact_metrics + - picard_CollectWgsMetrics + - picard_DownsampleSam + - picard_EstimateLibraryComplexity + - picard_FastqToSam + - picard_FilterSamReads + - picard_FixMateInformation + - picard_MarkDuplicates + - picard_MarkDuplicatesWithMateCigar + - picard_MeanQualityByCycle + - picard_MergeBamAlignment + - picard_MergeSamFiles + - picard_NormalizeFasta + - picard_QualityScoreDistribution + - picard_ReorderSam + - picard_ReplaceSamHeader + - picard_RevertOriginalBaseQualitiesAndAddMateCigar + - picard_RevertSam + - picard_SamToFastq + - picard_SortSam + - picard_ValidateSamFile + Galaxy wrapper id: picard + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard + Galaxy wrapper version: 3.1.1 + No. of tool users (5 years) (usegalaxy.eu): 386934 + No. of tool users (5 years) (usegalaxy.org): 366646 + No. of tool users (5 years) (usegalaxy.org.au): 56622 + No. of tool users (5 years) - all main servers: 810202 + No. of tool users (all time) (usegalaxy.eu): 399039 + No. of tool users (all time) (usegalaxy.org): 589980 + No. of tool users (all time) (usegalaxy.org.au): 62258 + No. of tool users (all time) - all main servers: 1051277 + Source: http://broadinstitute.github.io/picard/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11024 + Tool usage (5 years) (usegalaxy.org): 32000 + Tool usage (5 years) (usegalaxy.org.au): 2845 + Tool usage (5 years) - all main servers: 45869 + Tool usage (all time) (usegalaxy.eu): 11956 + Tool usage (all time) (usegalaxy.org): 57111 + Tool usage (all time) (usegalaxy.org.au): 3398 + Tool usage (all time) - all main servers: 72465 + ToolShed categories: + - SAM + ToolShed id: picard + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 31 + Tools available on Galaxy@Pasteur: 4 + Tools available on GalaxyTrakr: 31 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 31 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 31 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 31 + Tools available on UseGalaxy.cz: 31 + Tools available on UseGalaxy.eu: 31 + Tools available on UseGalaxy.fr: 31 + Tools available on UseGalaxy.no: 31 + Tools available on UseGalaxy.org (Main): 31 + Tools available on UseGalaxy.org.au: 31 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 31 + UseGalaxy.cz: 31 + UseGalaxy.eu: 31 + UseGalaxy.fr: 31 + UseGalaxy.no: 31 + UseGalaxy.or: 31 + biii: null + bio.tool description: Create a FASTQ file. + bio.tool id: picard_samtofastq + bio.tool ids: + - picard_samtofastq + - picard_replacesamheader + - picard_fastqtosam + - picard_reordersam + bio.tool name: picard_samtofastq +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-01-23' + Description: Compose a text parameter value using text, integer and float values + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pick_value + Galaxy wrapper id: pick_value + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 1607 + No. of tool users (5 years) (usegalaxy.org): 490 + No. of tool users (5 years) (usegalaxy.org.au): 127 + No. of tool users (5 years) - all main servers: 2224 + No. of tool users (all time) (usegalaxy.eu): 1607 + No. of tool users (all time) (usegalaxy.org): 490 + No. of tool users (all time) (usegalaxy.org.au): 127 + No. of tool users (all time) - all main servers: 2224 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 41 + Tool usage (5 years) (usegalaxy.org): 53 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 98 + Tool usage (all time) (usegalaxy.eu): 41 + Tool usage (all time) (usegalaxy.org): 53 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 98 + ToolShed categories: + - Text Manipulation + ToolShed id: pick_value + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 6 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 6 + Conda id: picrust + Conda version: 1.1.4 + Date of first commit of the suite: '2017-07-31' + Description: PICRUSt wrappers + EDAM operation: + - Phylogenetic reconstruction + - Expression analysis + - Genome annotation + - DNA barcoding + EDAM operation (no superclasses): + - Phylogenetic reconstruction + - Expression analysis + - Genome annotation + - DNA barcoding + EDAM topic: + - Metagenomics + - Microbial ecology + - Functional, regulatory and non-coding RNA + - Metagenomic sequencing + EDAM topic (no superclasses): + - Metagenomics + - Microbial ecology + - Functional, regulatory and non-coding RNA + - Metagenomic sequencing + Galaxy tool ids: + - picrust_categorize + - picrust_compare_biom + - picrust_format_tree_and_trait_table + - picrust_metagenome_contributions + - picrust_normalize_by_copy_number + - picrust_predict_metagenomes + Galaxy wrapper id: picrust + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust + Galaxy wrapper version: 1.1.1 + No. of tool users (5 years) (usegalaxy.eu): 867 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 2106 + No. of tool users (5 years) - all main servers: 2973 + No. of tool users (all time) (usegalaxy.eu): 1128 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 2106 + No. of tool users (all time) - all main servers: 3234 + Source: https://picrust.github.io/picrust/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 144 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 121 + Tool usage (5 years) - all main servers: 265 + Tool usage (all time) (usegalaxy.eu): 165 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 121 + Tool usage (all time) - all main servers: 286 + ToolShed categories: + - Metagenomics + ToolShed id: picrust + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 6 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 6 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 6 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 6 + UseGalaxy.no: 5 + UseGalaxy.or: 6 + biii: null + bio.tool description: PICRUSt (Phylogenetic Investigation of Communities by Reconstruction + of Unobserved States) is a bioinformatics software package designed to predict + metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full + genomes. + bio.tool id: picrust + bio.tool ids: + - picrust + bio.tool name: PICRUSt +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 7 + Conda id: picrust2 + Conda version: 2.5.3 + Date of first commit of the suite: '2021-11-07' + Description: 'PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction + of Unobserved States' + EDAM operation: + - Phylogenetic reconstruction + - Expression analysis + - Rarefaction + - Pathway analysis + EDAM operation (no superclasses): + - Phylogenetic reconstruction + - Expression analysis + - Rarefaction + - Pathway analysis + EDAM topic: + - Metagenomics + - Microbiology + - Phylogenetics + - Metagenomic sequencing + EDAM topic (no superclasses): + - Metagenomics + - Microbiology + - Phylogenetics + - Metagenomic sequencing + Galaxy tool ids: + - picrust2_add_descriptions + - picrust2_hsp + - picrust2_metagenome_pipeline + - picrust2_pathway_pipeline + - picrust2_pipeline + - picrust2_place_seqs + - picrust2_shuffle_predictions + Galaxy wrapper id: picrust2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 + Galaxy wrapper source: https://github.com/picrust/picrust2 + Galaxy wrapper version: 2.5.3 + No. of tool users (5 years) (usegalaxy.eu): 2532 + No. of tool users (5 years) (usegalaxy.org): 1 + No. of tool users (5 years) (usegalaxy.org.au): 1311 + No. of tool users (5 years) - all main servers: 3844 + No. of tool users (all time) (usegalaxy.eu): 2532 + No. of tool users (all time) (usegalaxy.org): 1 + No. of tool users (all time) (usegalaxy.org.au): 1311 + No. of tool users (all time) - all main servers: 3844 + Source: https://github.com/picrust/picrust2/wiki + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 382 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 83 + Tool usage (5 years) - all main servers: 466 + Tool usage (all time) (usegalaxy.eu): 382 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 83 + Tool usage (all time) - all main servers: 466 + ToolShed categories: + - Metagenomics + ToolShed id: picrust2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 7 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + UseGalaxy.or: 7 + biii: null + bio.tool description: PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction + of Unobserved States) is a software for predicting functional abundances based + only on marker gene sequences. + bio.tool id: picrust2 + bio.tool ids: + - picrust2 + bio.tool name: PICRUSt2 +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pilon + Conda version: '1.24' + Date of first commit of the suite: '2016-08-11' + Description: pilon is a tool for assembly improvement and variant analysis in bacteria + EDAM operation: + - Sequence assembly + - Analysis + - Read alignment + EDAM operation (no superclasses): + - Sequence assembly + - Analysis + EDAM topic: + - Assembly + EDAM topic (no superclasses): + - Assembly + Galaxy tool ids: + - pilon + Galaxy wrapper id: pilon + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon + Galaxy wrapper version: 1.20.1 + No. of tool users (5 years) (usegalaxy.eu): 9045 + No. of tool users (5 years) (usegalaxy.org): 7989 + No. of tool users (5 years) (usegalaxy.org.au): 3945 + No. of tool users (5 years) - all main servers: 20979 + No. of tool users (all time) (usegalaxy.eu): 9458 + No. of tool users (all time) (usegalaxy.org): 7989 + No. of tool users (all time) (usegalaxy.org.au): 4137 + No. of tool users (all time) - all main servers: 21584 + Source: https://github.com/broadinstitute/pilon/wiki + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1115 + Tool usage (5 years) (usegalaxy.org): 1070 + Tool usage (5 years) (usegalaxy.org.au): 726 + Tool usage (5 years) - all main servers: 2911 + Tool usage (all time) (usegalaxy.eu): 1144 + Tool usage (all time) (usegalaxy.org): 1070 + Tool usage (all time) (usegalaxy.org.au): 741 + Tool usage (all time) - all main servers: 2955 + ToolShed categories: + - Variant Analysis + ToolShed id: pilon + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Read alignment analysis to diagnose, report, and automatically + improve de novo genome assemblies. + bio.tool id: pilon + bio.tool ids: + - pilon + bio.tool name: pilon +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: pipelign + Conda version: '0.2' + Date of first commit of the suite: '2019-08-20' + Description: Multipe sequence alignment + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pipelign + Galaxy wrapper id: pipelign + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign + Galaxy wrapper version: '0.2' + No. of tool users (5 years) (usegalaxy.eu): 1245 + No. of tool users (5 years) (usegalaxy.org): 9046 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 10291 + No. of tool users (all time) (usegalaxy.eu): 1245 + No. of tool users (all time) (usegalaxy.org): 9046 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 10291 + Source: https://github.com/asmmhossain/pipelign/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 231 + Tool usage (5 years) (usegalaxy.org): 630 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 861 + Tool usage (all time) (usegalaxy.eu): 231 + Tool usage (all time) (usegalaxy.org): 630 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 861 + ToolShed categories: + - Next Gen Mappers + ToolShed id: pipelign + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: pizzly + Conda version: 0.37.3 + Date of first commit of the suite: '2017-09-03' + Description: Pizzly is a program for detecting gene fusions from RNA-Seq data of + cancer samples. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pizzly + Galaxy wrapper id: pizzly + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ + Galaxy wrapper version: 0.37.3.1 + No. of tool users (5 years) (usegalaxy.eu): 201 + No. of tool users (5 years) (usegalaxy.org): 998 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1199 + No. of tool users (all time) (usegalaxy.eu): 210 + No. of tool users (all time) (usegalaxy.org): 998 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1208 + Source: https://github.com/pmelsted/pizzly/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 23 + Tool usage (5 years) (usegalaxy.org): 76 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 99 + Tool usage (all time) (usegalaxy.eu): 24 + Tool usage (all time) (usegalaxy.org): 76 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 100 + ToolShed categories: + - Transcriptomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: plasflow + Conda version: 1.1.0 + Date of first commit of the suite: '2018-09-05' + Description: PlasFlow - Prediction of plasmid sequences in metagenomic contigs. + EDAM operation: + - Sequence analysis + EDAM operation (no superclasses): + - Sequence analysis + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - PlasFlow + Galaxy wrapper id: plasflow + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 37086 + No. of tool users (5 years) (usegalaxy.org): 6346 + No. of tool users (5 years) (usegalaxy.org.au): 3065 + No. of tool users (5 years) - all main servers: 46497 + No. of tool users (all time) (usegalaxy.eu): 37272 + No. of tool users (all time) (usegalaxy.org): 6346 + No. of tool users (all time) (usegalaxy.org.au): 3065 + No. of tool users (all time) - all main servers: 46683 + Source: https://github.com/smaegol/PlasFlow + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 711 + Tool usage (5 years) (usegalaxy.org): 583 + Tool usage (5 years) (usegalaxy.org.au): 61 + Tool usage (5 years) - all main servers: 1355 + Tool usage (all time) (usegalaxy.eu): 734 + Tool usage (all time) (usegalaxy.org): 583 + Tool usage (all time) (usegalaxy.org.au): 61 + Tool usage (all time) - all main servers: 1378 + ToolShed categories: + - Sequence Analysis + ToolShed id: plasflow + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: PlasFlow is a set of scripts used for prediction of plasmid + sequences in metagenomic contigs. + bio.tool id: plasflow + bio.tool ids: + - plasflow + bio.tool name: PlasFlow +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: plasmidfinder + Conda version: 2.1.6 + Date of first commit of the suite: '2022-09-19' + Description: '"PlasmidFinder provides the detection of replicons in the WGSand assigns + the plasmids under study to lineages that trace backthe information to the existing + knowledge on Inc groups and suggestspossible reference plasmids for each lineage"' + EDAM operation: + - Genome assembly + - Scaffolding + - Multilocus sequence typing + EDAM operation (no superclasses): + - Genome assembly + - Scaffolding + - Multilocus sequence typing + EDAM topic: + - Whole genome sequencing + - Sequence assembly + - Mapping + - Probes and primers + EDAM topic (no superclasses): + - Whole genome sequencing + - Sequence assembly + - Mapping + - Probes and primers + Galaxy tool ids: + - plasmidfinder + Galaxy wrapper id: plasmidfinder + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder + Galaxy wrapper version: 2.1.6 + No. of tool users (5 years) (usegalaxy.eu): 14652 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 101 + No. of tool users (5 years) - all main servers: 14753 + No. of tool users (all time) (usegalaxy.eu): 14652 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 101 + No. of tool users (all time) - all main servers: 14753 + Source: https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 251 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 18 + Tool usage (5 years) - all main servers: 269 + Tool usage (all time) (usegalaxy.eu): 251 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 18 + Tool usage (all time) - all main servers: 269 + ToolShed categories: + - Sequence Analysis + ToolShed id: plasmidfinder + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: PlasmidFinder is a tool for the identification and typing + of Plasmid Replicons in Whole-Genome Sequencing (WGS). + bio.tool id: PlasmidFinder + bio.tool ids: + - PlasmidFinder + bio.tool name: PlasmidFinder +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: plink + Conda version: 1.90b6.21 + Date of first commit of the suite: '2020-09-14' + Description: Whole genome association analysis toolset, designed to perform a range + of basic, large-scale analyses in a computationally efficient manner. + EDAM operation: + - Genetic variation analysis + EDAM operation (no superclasses): + - Genetic variation analysis + EDAM topic: + - GWAS study + EDAM topic (no superclasses): + - GWAS study + Galaxy tool ids: + - plink + Galaxy wrapper id: plink + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink + Galaxy wrapper version: 1.90b6.21 + No. of tool users (5 years) (usegalaxy.eu): 851 + No. of tool users (5 years) (usegalaxy.org): 249 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1100 + No. of tool users (all time) (usegalaxy.eu): 851 + No. of tool users (all time) (usegalaxy.org): 249 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1100 + Source: https://www.cog-genomics.org/plink + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 127 + Tool usage (5 years) (usegalaxy.org): 43 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 170 + Tool usage (all time) (usegalaxy.eu): 127 + Tool usage (all time) (usegalaxy.org): 43 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 170 + ToolShed categories: + - Genome-Wide Association Study + ToolShed id: plink + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Free, open-source whole genome association analysis toolset, + designed to perform a range of basic, large-scale analyses in a computationally + efficient manner. + bio.tool id: plink + bio.tool ids: + - plink + bio.tool name: PLINK +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: polypolish + Conda version: 0.6.0 + Date of first commit of the suite: '2022-09-22' + Description: '"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish + uses SAM files where each read has been aligned to all possible locations (not + just a single best location).This allows it to repair errors in repeat regions + that other alignment-based polishers cannot fix."' + EDAM operation: + - Genome assembly + - Read mapping + - Mapping assembly + - Sequencing error detection + EDAM operation (no superclasses): + - Genome assembly + - Read mapping + - Mapping assembly + - Sequencing error detection + EDAM topic: + - Sequence assembly + - Sequence composition, complexity and repeats + - Mapping + EDAM topic (no superclasses): + - Sequence assembly + - Sequence composition, complexity and repeats + - Mapping + Galaxy tool ids: + - polypolish + Galaxy wrapper id: polypolish + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish + Galaxy wrapper source: https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish + Galaxy wrapper version: 0.5.0 + No. of tool users (5 years) (usegalaxy.eu): 731 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 42 + No. of tool users (5 years) - all main servers: 773 + No. of tool users (all time) (usegalaxy.eu): 731 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 42 + No. of tool users (all time) - all main servers: 773 + Source: https://github.com/rrwick/Polypolish + Status: To update + Tool usage (5 years) (usegalaxy.eu): 86 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 90 + Tool usage (all time) (usegalaxy.eu): 86 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 90 + ToolShed categories: + - Sequence Analysis + ToolShed id: polypolish + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Polypolish is a tool for polishing genome assemblies with + short reads. Unlike other tools in this category, Polypolish uses SAM files where + each read has been aligned to all possible locations (not just a single best location). + This allows it to repair errors in repeat regions that other alignment-based polishers + cannot fix. + bio.tool id: Polypolish + bio.tool ids: + - Polypolish + bio.tool name: Polypolish +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: porechop + Conda version: 0.2.4 + Date of first commit of the suite: '2018-09-13' + Description: Porechop - Finding and removing adapters from Oxford Nanopore reads + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - porechop + Galaxy wrapper id: porechop + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 262015 + No. of tool users (5 years) (usegalaxy.org): 83623 + No. of tool users (5 years) (usegalaxy.org.au): 52558 + No. of tool users (5 years) - all main servers: 398196 + No. of tool users (all time) (usegalaxy.eu): 262852 + No. of tool users (all time) (usegalaxy.org): 83623 + No. of tool users (all time) (usegalaxy.org.au): 52558 + No. of tool users (all time) - all main servers: 399033 + Source: https://github.com/rrwick/Porechop + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2627 + Tool usage (5 years) (usegalaxy.org): 1918 + Tool usage (5 years) (usegalaxy.org.au): 1037 + Tool usage (5 years) - all main servers: 5582 + Tool usage (all time) (usegalaxy.eu): 2711 + Tool usage (all time) (usegalaxy.org): 1918 + Tool usage (all time) (usegalaxy.org.au): 1037 + Tool usage (all time) - all main servers: 5666 + ToolShed categories: + - Fasta Manipulation + - Fastq Manipulation + ToolShed id: porechop + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 13 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 13 + Available on UseGalaxy.org.au: 13 + Conda id: poretools + Conda version: 0.6.1a1 + Date of first commit of the suite: '2017-12-17' + Description: A flexible toolkit for exploring datasets generated by nanopore sequencing + devices from MinION for the purposes of quality control and downstream analysis. + EDAM operation: + - Nucleic acid sequence analysis + EDAM operation (no superclasses): + - Nucleic acid sequence analysis + EDAM topic: + - DNA + - Sequencing + EDAM topic (no superclasses): + - DNA + - Sequencing + Galaxy tool ids: + - poretools_events + - poretools_extract + - poretools_hist + - poretools_nucdist + - poretools_occupancy + - poretools_qualdist + - poretools_qualpos + - poretools_squiggle + - poretools_stats + - poretools_tabular + - poretools_times + - poretools_winner + - poretools_yield_plot + Galaxy wrapper id: poretools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools + Galaxy wrapper version: 0.6.1a1 + No. of tool users (5 years) (usegalaxy.eu): 19942 + No. of tool users (5 years) (usegalaxy.org): 33619 + No. of tool users (5 years) (usegalaxy.org.au): 9261 + No. of tool users (5 years) - all main servers: 62822 + No. of tool users (all time) (usegalaxy.eu): 20587 + No. of tool users (all time) (usegalaxy.org): 40808 + No. of tool users (all time) (usegalaxy.org.au): 9261 + No. of tool users (all time) - all main servers: 70656 + Source: https://poretools.readthedocs.io/en/latest/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1055 + Tool usage (5 years) (usegalaxy.org): 2183 + Tool usage (5 years) (usegalaxy.org.au): 365 + Tool usage (5 years) - all main servers: 3603 + Tool usage (all time) (usegalaxy.eu): 1245 + Tool usage (all time) (usegalaxy.org): 2594 + Tool usage (all time) (usegalaxy.org.au): 365 + Tool usage (all time) - all main servers: 4204 + ToolShed categories: + - Fasta Manipulation + - Fastq Manipulation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 13 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 13 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 13 + Tools available on UseGalaxy.org (Main): 13 + Tools available on UseGalaxy.org.au: 13 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 6 + UseGalaxy.eu: 13 + UseGalaxy.fr: 13 + UseGalaxy.no: 13 + UseGalaxy.or: 13 + biii: null + bio.tool description: Flexible toolkit for exploring datasets generated by nanopore + sequencing devices from MinION for the purposes of quality control and downstream + analysis. + bio.tool id: poretools + bio.tool ids: + - poretools + bio.tool name: Poretools +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 11 + Available on UseGalaxy.org.au: 0 + Conda id: presto + Conda version: 0.7.2 + Date of first commit of the suite: '2017-08-30' + Description: pRESTO toolkit for immune repertoire analysis. + EDAM operation: + - Nucleic acid sequence analysis + EDAM operation (no superclasses): + - Nucleic acid sequence analysis + EDAM topic: + - Sequencing + - DNA + - Immunology + EDAM topic (no superclasses): + - Sequencing + - DNA + - Immunology + Galaxy tool ids: + - presto_alignsets + - presto_assemblepairs + - presto_buildconsensus + - presto_collapseseq + - presto_filterseq + - presto_maskprimers + - presto_pairseq + - presto_parseheaders + - presto_parselog + - presto_partition + - prestor_abseq3 + Galaxy wrapper id: presto + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto + Galaxy wrapper version: 0.6.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 63244 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 63244 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 65177 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 65177 + Source: https://presto.readthedocs.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 1392 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1392 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 1599 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1599 + ToolShed categories: + - Sequence Analysis + ToolShed id: presto + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 11 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 11 + biii: null + bio.tool description: Integrated collection of platform-independent Python modules + for processing raw reads from high-throughput (next-generation) sequencing of + lymphocyte repertoires. + bio.tool id: presto + bio.tool ids: + - presto + bio.tool name: pRESTO +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 2 + Conda id: pretextgraph + Conda version: 0.0.6 + Date of first commit of the suite: '2021-04-05' + Description: Process genome contacts maps processing images. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pretext_graph + - pretext_map + - pretext_snapshot + Galaxy wrapper id: pretext + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext + Galaxy wrapper version: 0.0.6 + No. of tool users (5 years) (usegalaxy.eu): 3463 + No. of tool users (5 years) (usegalaxy.org): 1853 + No. of tool users (5 years) (usegalaxy.org.au): 1097 + No. of tool users (5 years) - all main servers: 6413 + No. of tool users (all time) (usegalaxy.eu): 3463 + No. of tool users (all time) (usegalaxy.org): 1853 + No. of tool users (all time) (usegalaxy.org.au): 1097 + No. of tool users (all time) - all main servers: 6413 + Source: https://github.com/wtsi-hpag/PretextSnapshot + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 538 + Tool usage (5 years) (usegalaxy.org): 256 + Tool usage (5 years) (usegalaxy.org.au): 70 + Tool usage (5 years) - all main servers: 864 + Tool usage (all time) (usegalaxy.eu): 538 + Tool usage (all time) (usegalaxy.org): 256 + Tool usage (all time) (usegalaxy.org.au): 70 + Tool usage (all time) - all main servers: 864 + ToolShed categories: + - Sequence Analysis + ToolShed id: suite_pretext + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 3 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: prinseq + Conda version: 0.20.4 + Date of first commit of the suite: '2016-05-30' + Description: PRINSEQ is a tool for easy and rapid quality control and data processing + of metagenomic and metatranscriptomic datasets + EDAM operation: + - Read pre-processing + - Sequence trimming + - Sequence contamination filtering + EDAM operation (no superclasses): + - Read pre-processing + - Sequence trimming + - Sequence contamination filtering + EDAM topic: + - Transcriptomics + - Metagenomics + - Genomics + EDAM topic (no superclasses): + - Transcriptomics + - Metagenomics + Galaxy tool ids: + - prinseq + Galaxy wrapper id: prinseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ + Galaxy wrapper version: '@TOOL_VERSION+galaxy2' + No. of tool users (5 years) (usegalaxy.eu): 10152 + No. of tool users (5 years) (usegalaxy.org): 10581 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 20733 + No. of tool users (all time) (usegalaxy.eu): 10626 + No. of tool users (all time) (usegalaxy.org): 10581 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 21207 + Source: http://prinseq.sourceforge.net/manual.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 253 + Tool usage (5 years) (usegalaxy.org): 1240 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1493 + Tool usage (all time) (usegalaxy.eu): 281 + Tool usage (all time) (usegalaxy.org): 1240 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1521 + ToolShed categories: + - Fastq Manipulation + - Metagenomics + ToolShed id: prinseq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: PRINSEQ is a sequence processing tool that can be used to + filter, reformat and trim genomic and metagenomic sequence data. It generates + summary statistics of the input in graphical and tabular formats that can be used + for quality control steps. PRINSEQ is available as both standalone and web-based + versions. + bio.tool id: prinseq + bio.tool ids: + - prinseq + bio.tool name: PRINSEQ +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: prodigal + Conda version: 2.6.3 + Date of first commit of the suite: '2024-03-14' + Description: A protein-coding gene prediction software tool for bacterial and archaeal + genomes + EDAM operation: + - Genome annotation + EDAM operation (no superclasses): + - Genome annotation + EDAM topic: + - Genomics + - Sequence analysis + EDAM topic (no superclasses): + - Genomics + - Sequence analysis + Galaxy tool ids: + - prodigal + Galaxy wrapper id: prodigal + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal + Galaxy wrapper version: 2.6.3 + No. of tool users (5 years) (usegalaxy.eu): 1902 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1902 + No. of tool users (all time) (usegalaxy.eu): 1902 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1902 + Source: https://github.com/hyattpd/Prodigal + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 167 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 167 + Tool usage (all time) (usegalaxy.eu): 167 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 167 + ToolShed categories: + - Genome annotation + ToolShed id: prodigal + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Fast, reliable protein-coding gene prediction for prokaryotic + genomes. + bio.tool id: prodigal + bio.tool ids: + - prodigal + bio.tool name: Prodigal +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: progressivemauve + Conda version: snapshot_2015_02_13 + Date of first commit of the suite: '2015-05-18' + Description: Mauve/ProgressiveMauve Multiple Sequence Aligner + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - progressivemauve + - xmfa2gff3 + Galaxy wrapper id: progressivemauve + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 2064 + No. of tool users (5 years) (usegalaxy.org): 2900 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4964 + No. of tool users (all time) (usegalaxy.eu): 2173 + No. of tool users (all time) (usegalaxy.org): 2900 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5073 + Source: http://darlinglab.org/mauve/user-guide/progressivemauve.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 678 + Tool usage (5 years) (usegalaxy.org): 1034 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1712 + Tool usage (all time) (usegalaxy.eu): 695 + Tool usage (all time) (usegalaxy.org): 1034 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1729 + ToolShed categories: + - Sequence Analysis + ToolShed id: progressivemauve + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: prokka + Conda version: 1.14.6 + Date of first commit of the suite: '2016-10-10' + Description: Rapid annotation of prokaryotic genomes + EDAM operation: + - Gene prediction + - Coding region prediction + - Genome annotation + EDAM operation (no superclasses): + - Coding region prediction + - Genome annotation + EDAM topic: + - Genomics + - Model organisms + - Virology + EDAM topic (no superclasses): + - Genomics + - Model organisms + - Virology + Galaxy tool ids: + - prokka + Galaxy wrapper id: prokka + Galaxy wrapper owner: crs4 + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ + Galaxy wrapper version: 1.14.6 + No. of tool users (5 years) (usegalaxy.eu): 464359 + No. of tool users (5 years) (usegalaxy.org): 313285 + No. of tool users (5 years) (usegalaxy.org.au): 131211 + No. of tool users (5 years) - all main servers: 908855 + No. of tool users (all time) (usegalaxy.eu): 476554 + No. of tool users (all time) (usegalaxy.org): 331256 + No. of tool users (all time) (usegalaxy.org.au): 141875 + No. of tool users (all time) - all main servers: 949685 + Source: http://github.com/tseemann/prokka + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 7475 + Tool usage (5 years) (usegalaxy.org): 11243 + Tool usage (5 years) (usegalaxy.org.au): 4358 + Tool usage (5 years) - all main servers: 23076 + Tool usage (all time) (usegalaxy.eu): 7721 + Tool usage (all time) (usegalaxy.org): 12384 + Tool usage (all time) (usegalaxy.org.au): 4947 + Tool usage (all time) - all main servers: 25052 + ToolShed categories: + - Sequence Analysis + ToolShed id: prokka + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Software tool to annotate bacterial, archaeal and viral genomes + quickly and produce standards-compliant output files. + bio.tool id: prokka + bio.tool ids: + - prokka + bio.tool name: Prokka +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: prot-scriber + Conda version: 0.1.6 + Date of first commit of the suite: '2022-05-10' + Description: Protein annotation of short human readable descriptions + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - prot_scriber + Galaxy wrapper id: prot-scriber + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber + Galaxy wrapper version: 0.1.6 + No. of tool users (5 years) (usegalaxy.eu): 10 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 10 + No. of tool users (all time) (usegalaxy.eu): 10 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 10 + Source: https://github.com/usadellab/prot-scriber + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - Proteomics + ToolShed id: prot_scriber + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteinortho + Conda version: 6.3.2 + Date of first commit of the suite: '2020-10-02' + Description: Proteinortho is a tool to detect orthologous proteins/genes within + different species. + EDAM operation: + - Sequence clustering + - Sequence analysis + EDAM operation (no superclasses): + - Sequence clustering + - Sequence analysis + EDAM topic: + - Comparative genomics + EDAM topic (no superclasses): + - Comparative genomics + Galaxy tool ids: + - proteinortho + - proteinortho_grab_proteins + - proteinortho_summary + Galaxy wrapper id: proteinortho + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho + Galaxy wrapper source: https://gitlab.com/paulklemm_PHD/proteinortho + Galaxy wrapper version: 6.3.1 + No. of tool users (5 years) (usegalaxy.eu): 3962 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3962 + No. of tool users (all time) (usegalaxy.eu): 3962 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3962 + Source: https://gitlab.com/paulklemm_PHD/proteinortho + Status: To update + Tool usage (5 years) (usegalaxy.eu): 501 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 501 + Tool usage (all time) (usegalaxy.eu): 501 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 501 + ToolShed categories: + - Proteomics + ToolShed id: proteinortho + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 1 + UseGalaxy.no: 3 + biii: null + bio.tool description: Proteinortho is a tool to detect orthologous genes within + different species + bio.tool id: proteinortho + bio.tool ids: + - proteinortho + bio.tool name: Proteinortho +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: psiclass + Conda version: 1.0.3 + Date of first commit of the suite: '2023-09-06' + Description: PsiCLASS is a reference-based transcriptome assembler for single or + multiple RNA-seq samples. + EDAM operation: + - Transcriptome assembly + EDAM operation (no superclasses): + - Transcriptome assembly + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - psiclass + Galaxy wrapper id: psiclass + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass + Galaxy wrapper version: 1.0.3 + No. of tool users (5 years) (usegalaxy.eu): 24 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 24 + No. of tool users (all time) (usegalaxy.eu): 24 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 24 + Source: https://github.com/splicebox/PsiCLASS + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Transcriptomics + ToolShed id: psiclass + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Reference-based transcriptome assembler for single or multiple + RNA-seq samples + bio.tool id: psiclass + bio.tool ids: + - psiclass + bio.tool name: PsiCLASS +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pureclip + Conda version: 1.3.1 + Date of first commit of the suite: '2018-04-26' + Description: PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP + data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pureclip + Galaxy wrapper id: pureclip + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip + Galaxy wrapper version: 1.0.4 + No. of tool users (5 years) (usegalaxy.eu): 1319 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1319 + No. of tool users (all time) (usegalaxy.eu): 1507 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1507 + Source: https://github.com/skrakau/PureCLIP + Status: To update + Tool usage (5 years) (usegalaxy.eu): 81 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 81 + Tool usage (all time) (usegalaxy.eu): 92 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 92 + ToolShed categories: + - Sequence Analysis + - RNA + - CLIP-seq + ToolShed id: pureclip + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: purge_dups + Conda version: 1.2.6 + Date of first commit of the suite: '2021-02-03' + Description: Purge haplotigs and overlaps in an assembly based on read depth + EDAM operation: + - Genome assembly + - Read binning + - Scaffolding + EDAM operation (no superclasses): + - Genome assembly + - Read binning + - Scaffolding + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - purge_dups + Galaxy wrapper id: purge_dups + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups + Galaxy wrapper version: 1.2.6 + No. of tool users (5 years) (usegalaxy.eu): 17782 + No. of tool users (5 years) (usegalaxy.org): 853 + No. of tool users (5 years) (usegalaxy.org.au): 2224 + No. of tool users (5 years) - all main servers: 20859 + No. of tool users (all time) (usegalaxy.eu): 17782 + No. of tool users (all time) (usegalaxy.org): 853 + No. of tool users (all time) (usegalaxy.org.au): 2224 + No. of tool users (all time) - all main servers: 20859 + Source: https://github.com/dfguan/purge_dups + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 287 + Tool usage (5 years) (usegalaxy.org): 65 + Tool usage (5 years) (usegalaxy.org.au): 65 + Tool usage (5 years) - all main servers: 417 + Tool usage (all time) (usegalaxy.eu): 287 + Tool usage (all time) (usegalaxy.org): 65 + Tool usage (all time) (usegalaxy.org.au): 65 + Tool usage (all time) - all main servers: 417 + ToolShed categories: + - Assembly + ToolShed id: purge_dups + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'Identifying and removing haplotypic duplication in primary + genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: + script to generate a configuration file used by run_purge_dups.py | purge haplotigs + and overlaps in an assembly based on read depth | Given a primary assembly pri_asm + and an alternative assembly hap_asm (optional, if you have one), follow the steps + shown below to build your own purge_dups pipeline, steps with same number can + be run simultaneously. Among all the steps, although step 4 is optional, we highly + recommend our users to do so, because assemblers may produce overrepresented seqeuences. + In such a case, The final step 4 can be applied to remove those seqeuences' + bio.tool id: purge_dups + bio.tool ids: + - purge_dups + bio.tool name: purge_dups +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pycoqc + Conda version: 2.5.2 + Date of first commit of the suite: '2021-03-02' + Description: QC metrics for ONT Basecalling + EDAM operation: + - Sequencing quality control + - Statistical calculation + EDAM operation (no superclasses): + - Sequencing quality control + - Statistical calculation + EDAM topic: + - Sequence analysis + - Data quality management + - Sequencing + EDAM topic (no superclasses): + - Sequence analysis + - Data quality management + - Sequencing + Galaxy tool ids: + - pycoqc + Galaxy wrapper id: pycoqc + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc + Galaxy wrapper version: 2.5.2 + No. of tool users (5 years) (usegalaxy.eu): 22742 + No. of tool users (5 years) (usegalaxy.org): 2159 + No. of tool users (5 years) (usegalaxy.org.au): 776 + No. of tool users (5 years) - all main servers: 25677 + No. of tool users (all time) (usegalaxy.eu): 22742 + No. of tool users (all time) (usegalaxy.org): 2159 + No. of tool users (all time) (usegalaxy.org.au): 776 + No. of tool users (all time) - all main servers: 25677 + Source: https://github.com/tleonardi/pycoQC + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 557 + Tool usage (5 years) (usegalaxy.org): 716 + Tool usage (5 years) (usegalaxy.org.au): 448 + Tool usage (5 years) - all main servers: 1721 + Tool usage (all time) (usegalaxy.eu): 557 + Tool usage (all time) (usegalaxy.org): 716 + Tool usage (all time) (usegalaxy.org.au): 448 + Tool usage (all time) - all main servers: 1721 + ToolShed categories: + - Nanopore + ToolShed id: pycoqc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: PycoQC computes metrics and generates interactive QC plots + for Oxford Nanopore technologies sequencing data. + bio.tool id: pycoqc + bio.tool ids: + - pycoqc + bio.tool name: pycoQC +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pyega3 + Conda version: 5.2.0 + Date of first commit of the suite: '2022-10-13' + Description: EGA python client uses the EGA REST API to download authorized datasets + and files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pyega3 + Galaxy wrapper id: pyega3 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 + Galaxy wrapper version: 5.0.2 + No. of tool users (5 years) (usegalaxy.eu): 2716 + No. of tool users (5 years) (usegalaxy.org): 134 + No. of tool users (5 years) (usegalaxy.org.au): 40 + No. of tool users (5 years) - all main servers: 2890 + No. of tool users (all time) (usegalaxy.eu): 2716 + No. of tool users (all time) (usegalaxy.org): 134 + No. of tool users (all time) (usegalaxy.org.au): 40 + No. of tool users (all time) - all main servers: 2890 + Source: https://github.com/EGA-archive/ega-download-client + Status: To update + Tool usage (5 years) (usegalaxy.eu): 104 + Tool usage (5 years) (usegalaxy.org): 43 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 148 + Tool usage (all time) (usegalaxy.eu): 104 + Tool usage (all time) (usegalaxy.org): 43 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 148 + ToolShed categories: + - Data Source + ToolShed id: ega_download_client + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pygenometracks + Conda version: '3.9' + Date of first commit of the suite: '2020-03-27' + Description: 'pyGenomeTracks: Standalone program and library to plot beautiful genome + browser tracks.' + EDAM operation: + - Visualisation + - Formatting + EDAM operation (no superclasses): + - Visualisation + - Formatting + EDAM topic: + - Model organisms + - Imaging + - Workflows + EDAM topic (no superclasses): + - Model organisms + - Imaging + - Workflows + Galaxy tool ids: + - pygenomeTracks + Galaxy wrapper id: pygenometracks + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks + Galaxy wrapper version: '3.8' + No. of tool users (5 years) (usegalaxy.eu): 12858 + No. of tool users (5 years) (usegalaxy.org): 8092 + No. of tool users (5 years) (usegalaxy.org.au): 3238 + No. of tool users (5 years) - all main servers: 24188 + No. of tool users (all time) (usegalaxy.eu): 13232 + No. of tool users (all time) (usegalaxy.org): 8092 + No. of tool users (all time) (usegalaxy.org.au): 3238 + No. of tool users (all time) - all main servers: 24562 + Source: https://github.com/deeptools/pyGenomeTracks + Status: To update + Tool usage (5 years) (usegalaxy.eu): 986 + Tool usage (5 years) (usegalaxy.org): 943 + Tool usage (5 years) (usegalaxy.org.au): 124 + Tool usage (5 years) - all main servers: 2053 + Tool usage (all time) (usegalaxy.eu): 996 + Tool usage (all time) (usegalaxy.org): 943 + Tool usage (all time) (usegalaxy.org.au): 124 + Tool usage (all time) - all main servers: 2063 + ToolShed categories: + - Visualization + ToolShed id: pygenometracks + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: reproducible plots for multivariate genomic data sets.Standalone + program and library to plot beautiful genome browser tracks.pyGenomeTracks aims + to produce high-quality genome browser tracks that are highly customizable. Currently, + it is possible to plot:. + bio.tool id: pygenometracks + bio.tool ids: + - pygenometracks + bio.tool name: pyGenomeTracks +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pysradb + Conda version: 2.2.2 + Date of first commit of the suite: '2022-11-10' + Description: pysradb allows to retrieve metadata, such as run accession numbers, + from SRA and ENA based on multiple criteria. + EDAM operation: + - Deposition + - Data retrieval + EDAM operation (no superclasses): + - Deposition + - Data retrieval + EDAM topic: + - Sequencing + - Gene transcripts + - Bioinformatics + EDAM topic (no superclasses): + - Sequencing + - Gene transcripts + - Bioinformatics + Galaxy tool ids: + - pysradb_search + Galaxy wrapper id: pysradb + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb + Galaxy wrapper version: 1.4.2 + No. of tool users (5 years) (usegalaxy.eu): 163 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 163 + No. of tool users (all time) (usegalaxy.eu): 163 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 163 + Source: https://github.com/saketkc/pysradb + Status: To update + Tool usage (5 years) (usegalaxy.eu): 35 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 35 + Tool usage (all time) (usegalaxy.eu): 35 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 35 + ToolShed categories: + - Sequence Analysis + ToolShed id: pysradb_search + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Python package to query next-generation sequencing metadata + and data from NCBI Sequence Read Archive. + bio.tool id: pysradb + bio.tool ids: + - pysradb + bio.tool name: pysradb +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: qfilt + Conda version: 0.0.1 + Date of first commit of the suite: '2018-06-06' + Description: Filter sequencing data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - qfilt + Galaxy wrapper id: qfilt + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt + Galaxy wrapper version: 1.0.0+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/veg/qfilt + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Fastq Manipulation + ToolShed id: qfilt + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: qiime + Conda version: 1.9.1 + Date of first commit of the suite: '2017-01-25' + Description: QIIME to perform microbial community analysis + EDAM operation: + - Demultiplexing + - Visualisation + - Taxonomic classification + - Phylogenetic analysis + - Sequencing quality control + EDAM operation (no superclasses): + - Demultiplexing + - Visualisation + - Taxonomic classification + - Phylogenetic analysis + - Sequencing quality control + EDAM topic: + - Microbial ecology + - Phylogeny + - Metagenomics + - Metatranscriptomics + EDAM topic (no superclasses): + - Microbial ecology + - Phylogeny + - Metagenomics + - Metatranscriptomics + Galaxy tool ids: + - qiime_collapse_samples + - qiime_make_otu_table + Galaxy wrapper id: qiime_add_on + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 2092 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 2 + No. of tool users (5 years) - all main servers: 2094 + No. of tool users (all time) (usegalaxy.eu): 2342 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 2 + No. of tool users (all time) - all main servers: 2344 + Source: http://www.qiime.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 209 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 210 + Tool usage (all time) (usegalaxy.eu): 238 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 239 + ToolShed categories: + - Metagenomics + ToolShed id: qiime + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + biii: null + bio.tool description: QIIME 2 is a next-generation microbiome bioinformatics platform + that is extensible, free, open source, and community developed. + bio.tool id: qiime_add_on + bio.tool ids: + - qiime_core + - qiime_add_on + bio.tool name: qiime_add_on +- Available on UseGalaxy.eu: 32 + Available on UseGalaxy.fr: 32 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: qiime + Conda version: 1.9.1 + Date of first commit of the suite: '2017-06-14' + Description: QIIME to perform microbial community analysis + EDAM operation: + - Demultiplexing + - Visualisation + - Taxonomic classification + - Phylogenetic analysis + - Sequencing quality control + EDAM operation (no superclasses): + - Demultiplexing + - Visualisation + - Taxonomic classification + - Phylogenetic analysis + - Sequencing quality control + EDAM topic: + - Microbial ecology + - Phylogeny + - Metagenomics + - Metatranscriptomics + EDAM topic (no superclasses): + - Microbial ecology + - Phylogeny + - Metagenomics + - Metatranscriptomics + Galaxy tool ids: + - qiime_align_seqs + - qiime_alpha_diversity + - qiime_alpha_rarefaction + - qiime_assign_taxonomy + - qiime_beta_diversity + - qiime_beta_diversity_through_plots + - qiime_compare_categories + - qiime_core_diversity + - qiime_count_seqs + - qiime_extract_barcodes + - qiime_filter_alignment + - qiime_filter_fasta + - qiime_filter_otus_from_otu_table + - qiime_filter_samples_from_otu_table + - qiime_filter_taxa_from_otu_table + - qiime_jackknifed_beta_diversity + - qiime_make_emperor + - qiime_make_otu_heatmap + - qiime_make_phylogeny + - qiime_multiple_join_paired_ends + - qiime_multiple_split_libraries_fastq + - qiime_pick_closed_reference_otus + - qiime_pick_open_reference_otus + - qiime_pick_otus + - qiime_pick_rep_set + - qiime_plot_taxa_summary + - qiime_split_libraries + - qiime_split_libraries_fastq + - qiime_summarize_taxa + - qiime_summarize_taxa_through_plots + - qiime_upgma_cluster + - qiime_validate_mapping_file + Galaxy wrapper id: qiime_core + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 31825 + No. of tool users (5 years) (usegalaxy.org): 1 + No. of tool users (5 years) (usegalaxy.org.au): 14 + No. of tool users (5 years) - all main servers: 31840 + No. of tool users (all time) (usegalaxy.eu): 34677 + No. of tool users (all time) (usegalaxy.org): 1 + No. of tool users (all time) (usegalaxy.org.au): 14 + No. of tool users (all time) - all main servers: 34692 + Source: http://www.qiime.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3375 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 3380 + Tool usage (all time) (usegalaxy.eu): 3785 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 3790 + ToolShed categories: + - Metagenomics + ToolShed id: qiime + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 31 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 31 + Tools available on UseGalaxy.eu: 32 + Tools available on UseGalaxy.fr: 32 + Tools available on UseGalaxy.no: 31 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 31 + UseGalaxy.eu: 32 + UseGalaxy.fr: 1 + UseGalaxy.no: 31 + biii: null + bio.tool description: "QIIME 2\u2122 is a next-generation microbiome bioinformatics\ + \ platform that is extensible, free, open source, and community developed." + bio.tool id: qiime_core + bio.tool ids: + - qiime_core + bio.tool name: qiime_core +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: unzip + Conda version: null + Date of first commit of the suite: '2022-10-06' + Description: Extract vizualization from QIIME artifacts + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - qiime_extract_viz + Galaxy wrapper id: qiime_extract_viz + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 17 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 17 + No. of tool users (all time) (usegalaxy.eu): 17 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 17 + Source: http://www.qiime.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Metagenomics + ToolShed id: qiime_extract_viz + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-qqman + Conda version: 0.1.4 + Date of first commit of the suite: '2020-10-07' + Description: null + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - qq_manhattan + Galaxy wrapper id: qq_tools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools + Galaxy wrapper source: null + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://CRAN.R-project.org/package=qqman + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Visualization + - Variant Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 4 + Conda id: qualimap + Conda version: '2.3' + Date of first commit of the suite: '2019-10-10' + Description: Qualimap 2 is a platform-independent application written in Java andR + that facilitates the quality control of alignment sequencing data and itsderivatives + like feature counts. + EDAM operation: + - Sequencing quality control + EDAM operation (no superclasses): + - Sequencing quality control + EDAM topic: + - Data quality management + EDAM topic (no superclasses): + - Data quality management + Galaxy tool ids: + - qualimap_bamqc + - qualimap_counts + - qualimap_multi_bamqc + - qualimap_rnaseq + Galaxy wrapper id: qualimap + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap + Galaxy wrapper version: '2.3' + No. of tool users (5 years) (usegalaxy.eu): 684820 + No. of tool users (5 years) (usegalaxy.org): 90503 + No. of tool users (5 years) (usegalaxy.org.au): 29018 + No. of tool users (5 years) - all main servers: 804341 + No. of tool users (all time) (usegalaxy.eu): 684820 + No. of tool users (all time) (usegalaxy.org): 90503 + No. of tool users (all time) (usegalaxy.org.au): 29018 + No. of tool users (all time) - all main servers: 804341 + Source: http://qualimap.bioinfo.cipf.es/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 3239 + Tool usage (5 years) (usegalaxy.org): 3881 + Tool usage (5 years) (usegalaxy.org.au): 826 + Tool usage (5 years) - all main servers: 7946 + Tool usage (all time) (usegalaxy.eu): 3239 + Tool usage (all time) (usegalaxy.org): 3881 + Tool usage (all time) (usegalaxy.org.au): 826 + Tool usage (all time) - all main servers: 7946 + ToolShed categories: + - Sequence Analysis + - Transcriptomics + - SAM + ToolShed id: qualimap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 4 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 4 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 4 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 4 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 4 + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 1 + UseGalaxy.no: 4 + UseGalaxy.or: 4 + biii: null + bio.tool description: Platform-independent application written in Java and R that + provides both a Graphical User Inteface (GUI) and a command-line interface to + facilitate the quality control of alignment sequencing data. + bio.tool id: qualimap + bio.tool ids: + - qualimap + bio.tool name: QualiMap +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: quast + Conda version: 5.2.0 + Date of first commit of the suite: '2018-02-10' + Description: Quast (Quality ASsessment Tool) evaluates genome assemblies. + EDAM operation: + - Visualisation + - Sequence assembly validation + EDAM operation (no superclasses): + - Visualisation + - Sequence assembly validation + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - quast + Galaxy wrapper id: quast + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast + Galaxy wrapper version: 5.2.0 + No. of tool users (5 years) (usegalaxy.eu): 67737 + No. of tool users (5 years) (usegalaxy.org): 51925 + No. of tool users (5 years) (usegalaxy.org.au): 32003 + No. of tool users (5 years) - all main servers: 151665 + No. of tool users (all time) (usegalaxy.eu): 69738 + No. of tool users (all time) (usegalaxy.org): 56602 + No. of tool users (all time) (usegalaxy.org.au): 34145 + No. of tool users (all time) - all main servers: 160485 + Source: http://quast.bioinf.spbau.ru/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 7787 + Tool usage (5 years) (usegalaxy.org): 9692 + Tool usage (5 years) (usegalaxy.org.au): 3890 + Tool usage (5 years) - all main servers: 21369 + Tool usage (all time) (usegalaxy.eu): 7971 + Tool usage (all time) (usegalaxy.org): 10646 + Tool usage (all time) (usegalaxy.org.au): 4127 + Tool usage (all time) - all main servers: 22744 + ToolShed categories: + - Assembly + ToolShed id: quast + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: QUAST stands for QUality ASsessment Tool. It evaluates a + quality of genome assemblies by computing various metrics and providing nice reports. + bio.tool id: quast + bio.tool ids: + - quast + bio.tool name: QUAST +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: requests + Conda version: null + Date of first commit of the suite: '2023-10-11' + Description: Contains a tool to query the IMPC database. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - query_impc + Galaxy wrapper id: query_impc + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc + Galaxy wrapper source: https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc + Galaxy wrapper version: 0.9.0 + No. of tool users (5 years) (usegalaxy.eu): 3 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3 + No. of tool users (all time) (usegalaxy.eu): 3 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3 + Source: https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Convert Formats + - Web Services + ToolShed id: query_impc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: python + Conda version: null + Date of first commit of the suite: '2017-07-18' + Description: Loads tabular files into a SQLite DB to perform a SQL query producing + a tabular output + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - filter_tabular + - query_tabular + - sqlite_to_tabular + Galaxy wrapper id: query_tabular + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular + Galaxy wrapper version: 3.3.1 + No. of tool users (5 years) (usegalaxy.eu): 130124 + No. of tool users (5 years) (usegalaxy.org): 11135 + No. of tool users (5 years) (usegalaxy.org.au): 5939 + No. of tool users (5 years) - all main servers: 147198 + No. of tool users (all time) (usegalaxy.eu): 135361 + No. of tool users (all time) (usegalaxy.org): 11135 + No. of tool users (all time) (usegalaxy.org.au): 5939 + No. of tool users (all time) - all main servers: 152435 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1265 + Tool usage (5 years) (usegalaxy.org): 922 + Tool usage (5 years) (usegalaxy.org.au): 153 + Tool usage (5 years) - all main servers: 2340 + Tool usage (all time) (usegalaxy.eu): 1305 + Tool usage (all time) (usegalaxy.org): 922 + Tool usage (all time) (usegalaxy.org.au): 153 + Tool usage (all time) - all main servers: 2380 + ToolShed categories: + - Text Manipulation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 3 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 1 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: quickmerge + Conda version: '0.3' + Date of first commit of the suite: '2022-07-08' + Description: Merge long-read and hybrid assemblies to increase contiguity + EDAM operation: + - Genome assembly + - Scaffolding + - De-novo assembly + - Genotyping + EDAM operation (no superclasses): + - Genome assembly + - Scaffolding + - De-novo assembly + - Genotyping + EDAM topic: + - Structural variation + - Sequence assembly + - DNA polymorphism + - Whole genome sequencing + - Genotype and phenotype + EDAM topic (no superclasses): + - Structural variation + - Sequence assembly + - DNA polymorphism + - Whole genome sequencing + - Genotype and phenotype + Galaxy tool ids: + - quickmerge + Galaxy wrapper id: quickmerge + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge + Galaxy wrapper version: '0.3' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/mahulchak/quickmerge + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Assembly + ToolShed id: quickmerge + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.no: 1 + biii: null + bio.tool description: Quickmerge is a program that uses complementary information + from genomes assembled with long reads in order to improve contiguity, and works + with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge + will even work with hybrid assemblies made by combining long reads and Illumina + short reads. + bio.tool id: quickmerge + bio.tool ids: + - quickmerge + bio.tool name: quickmerge +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: r-raceid + Conda version: 0.1.3 + Date of first commit of the suite: '2021-04-14' + Description: RaceID3, StemID2, FateID - scRNA analysis + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - raceid_clustering + - raceid_filtnormconf + - raceid_inspectclusters + - raceid_inspecttrajectory + - raceid_trajectory + Galaxy wrapper id: raceid + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 + Galaxy wrapper version: 0.2.3 + No. of tool users (5 years) (usegalaxy.eu): 3077 + No. of tool users (5 years) (usegalaxy.org): 2856 + No. of tool users (5 years) (usegalaxy.org.au): 1977 + No. of tool users (5 years) - all main servers: 7910 + No. of tool users (all time) (usegalaxy.eu): 4581 + No. of tool users (all time) (usegalaxy.org): 2856 + No. of tool users (all time) (usegalaxy.org.au): 1977 + No. of tool users (all time) - all main servers: 9414 + Source: https://github.com/dgrun/RaceID3_StemID2_package/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 395 + Tool usage (5 years) (usegalaxy.org): 1093 + Tool usage (5 years) (usegalaxy.org.au): 19 + Tool usage (5 years) - all main servers: 1507 + Tool usage (all time) (usegalaxy.eu): 518 + Tool usage (all time) (usegalaxy.org): 1093 + Tool usage (all time) (usegalaxy.org.au): 19 + Tool usage (all time) - all main servers: 1630 + ToolShed categories: + - Single Cell + - Transcriptomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 1 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: ragtag + Conda version: 2.1.0 + Date of first commit of the suite: '2021-11-10' + Description: Reference-guided scaffolding of draft genomes tool. + EDAM operation: + - Genome assembly + EDAM operation (no superclasses): + - Genome assembly + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - ragtag + Galaxy wrapper id: ragtag + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag + Galaxy wrapper version: 2.1.0 + No. of tool users (5 years) (usegalaxy.eu): 4844 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 7 + No. of tool users (5 years) - all main servers: 4851 + No. of tool users (all time) (usegalaxy.eu): 4844 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 7 + No. of tool users (all time) - all main servers: 4851 + Source: https://github.com/malonge/RagTag + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 480 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 483 + Tool usage (all time) (usegalaxy.eu): 480 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 483 + ToolShed categories: + - Assembly + ToolShed id: ragtag + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: RagTag is a collection of software tools for scaffolding and + improving modern genome assemblies. + bio.tool id: ragtag + bio.tool ids: + - ragtag + bio.tool name: ragtag +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: rapidnj + Conda version: 2.3.2 + Date of first commit of the suite: '2020-05-11' + Description: Galaxy wrapper for the RapidNJ tool + EDAM operation: + - Phylogenetic tree generation + EDAM operation (no superclasses): [] + EDAM topic: + - Phylogeny + EDAM topic (no superclasses): + - Phylogeny + Galaxy tool ids: + - rapidnj + Galaxy wrapper id: rapidnj + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj + Galaxy wrapper version: 2.3.2 + No. of tool users (5 years) (usegalaxy.eu): 339 + No. of tool users (5 years) (usegalaxy.org): 1737 + No. of tool users (5 years) (usegalaxy.org.au): 6 + No. of tool users (5 years) - all main servers: 2082 + No. of tool users (all time) (usegalaxy.eu): 339 + No. of tool users (all time) (usegalaxy.org): 1737 + No. of tool users (all time) (usegalaxy.org.au): 6 + No. of tool users (all time) - all main servers: 2082 + Source: https://birc.au.dk/software/rapidnj/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 30 + Tool usage (5 years) (usegalaxy.org): 256 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 287 + Tool usage (all time) (usegalaxy.eu): 30 + Tool usage (all time) (usegalaxy.org): 256 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 287 + ToolShed categories: + - Phylogenetics + ToolShed id: rapidnj + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool for fast canonical neighbor-joining tree construction. + bio.tool id: rapidnj + bio.tool ids: + - rapidnj + bio.tool name: RapidNJ +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rasusa + Conda version: 2.1.0 + Date of first commit of the suite: '2024-02-16' + Description: Randomly subsample sequencing reads to a specified coverage + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rasusa + Galaxy wrapper id: rasusa + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa + Galaxy wrapper version: 2.0.0 + No. of tool users (5 years) (usegalaxy.eu): 42 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 42 + No. of tool users (all time) (usegalaxy.eu): 42 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 42 + Source: https://github.com/mbhall88/rasusa + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Sequence Analysis + ToolShed id: rasusa + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Produces an unbiased subsample of your reads + bio.tool id: rasusa + bio.tool ids: + - rasusa + bio.tool name: rasusa +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: raven-assembler + Conda version: 1.8.3 + Date of first commit of the suite: '2020-11-04' + Description: Raven is a de novo genome assembler for long uncorrected reads. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - raven + Galaxy wrapper id: raven + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven + Galaxy wrapper version: 1.8.3 + No. of tool users (5 years) (usegalaxy.eu): 9477 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 10585 + No. of tool users (5 years) - all main servers: 20062 + No. of tool users (all time) (usegalaxy.eu): 9477 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 10585 + No. of tool users (all time) - all main servers: 20062 + Source: https://github.com/lbcb-sci/raven + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 438 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 182 + Tool usage (5 years) - all main servers: 620 + Tool usage (all time) (usegalaxy.eu): 438 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 182 + Tool usage (all time) - all main servers: 620 + ToolShed categories: + - Assembly + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: raxml + Conda version: 8.2.13 + Date of first commit of the suite: '2015-11-05' + Description: RAxML - A Maximum Likelihood based phylogenetic inference + EDAM operation: + - Sequence analysis + - Phylogenetic tree analysis + EDAM operation (no superclasses): + - Sequence analysis + EDAM topic: + - Phylogenetics + - Sequence analysis + EDAM topic (no superclasses): + - Phylogenetics + Galaxy tool ids: + - raxml + Galaxy wrapper id: raxml + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml + Galaxy wrapper version: 8.2.12 + No. of tool users (5 years) (usegalaxy.eu): 10905 + No. of tool users (5 years) (usegalaxy.org): 5100 + No. of tool users (5 years) (usegalaxy.org.au): 4955 + No. of tool users (5 years) - all main servers: 20960 + No. of tool users (all time) (usegalaxy.eu): 10905 + No. of tool users (all time) (usegalaxy.org): 5114 + No. of tool users (all time) (usegalaxy.org.au): 6094 + No. of tool users (all time) - all main servers: 22113 + Source: http://www.exelixis-lab.org/web/software/raxml/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 966 + Tool usage (5 years) (usegalaxy.org): 587 + Tool usage (5 years) (usegalaxy.org.au): 765 + Tool usage (5 years) - all main servers: 2318 + Tool usage (all time) (usegalaxy.eu): 966 + Tool usage (all time) (usegalaxy.org): 587 + Tool usage (all time) (usegalaxy.org.au): 892 + Tool usage (all time) - all main servers: 2445 + ToolShed categories: + - Phylogenetics + ToolShed id: raxml + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool for Phylogenetic Analysis and Post-Analysis of Large + Phylogenies. + bio.tool id: raxml + bio.tool ids: + - raxml + bio.tool name: RAxML +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rcorrector + Conda version: 1.0.7 + Date of first commit of the suite: '2018-05-02' + Description: Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction + method for RNA-seq data. + EDAM operation: + - Sequencing error detection + EDAM operation (no superclasses): + - Sequencing error detection + EDAM topic: + - RNA + - RNA-Seq + - Sequencing + EDAM topic (no superclasses): + - RNA + - RNA-Seq + Galaxy tool ids: + - rcorrector + Galaxy wrapper id: rcorrector + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector + Galaxy wrapper version: 1.0.3+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 655 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 655 + No. of tool users (all time) (usegalaxy.eu): 655 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 655 + Source: https://github.com/mourisl/Rcorrector + Status: To update + Tool usage (5 years) (usegalaxy.eu): 57 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 57 + Tool usage (all time) (usegalaxy.eu): 57 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 57 + ToolShed categories: + - Fastq Manipulation + ToolShed id: rcorrector + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: This is a kmer-based error correction method for RNA-seq data. + It can also be applied to other types of sequencing data where the read coverage + is non-uniform, such as single-cell sequencing. + bio.tool id: rcorrector + bio.tool ids: + - rcorrector + bio.tool name: Rcorrector +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: read-it-and-keep + Conda version: 0.3.0 + Date of first commit of the suite: '2022-01-28' + Description: Rapid decontamination of SARS-CoV-2 sequencing reads + EDAM operation: + - Filtering + - Genome alignment + EDAM operation (no superclasses): + - Filtering + - Genome alignment + EDAM topic: + - Pathology + - Genomics + EDAM topic (no superclasses): + - Pathology + - Genomics + Galaxy tool ids: + - read_it_and_keep + Galaxy wrapper id: read_it_and_keep + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep + Galaxy wrapper version: 0.2.2 + No. of tool users (5 years) (usegalaxy.eu): 3710 + No. of tool users (5 years) (usegalaxy.org): 7 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3717 + No. of tool users (all time) (usegalaxy.eu): 3710 + No. of tool users (all time) (usegalaxy.org): 7 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3717 + Source: https://github.com/GenomePathogenAnalysisService/read-it-and-keep + Status: To update + Tool usage (5 years) (usegalaxy.eu): 80 + Tool usage (5 years) (usegalaxy.org): 6 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 86 + Tool usage (all time) (usegalaxy.eu): 80 + Tool usage (all time) (usegalaxy.org): 6 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 86 + ToolShed categories: + - Sequence Analysis + ToolShed id: read_it_and_keep + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Read contamination removal + bio.tool id: read_it_and_keep + bio.tool ids: + - read_it_and_keep + bio.tool name: read_it_and_keep +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: recentrifuge + Conda version: 1.15.0 + Date of first commit of the suite: '2022-05-04' + Description: '"With Recentrifuge, researchers can analyze results from taxonomic + classifiers using interactive charts with emphasis on the confidence level of + the classifications.In addition to contamination-subtracted samples.Recentrifuge + provides shared and exclusive taxa per sample,thus enabling robust contamination + removal and comparative analysis in environmental and clinical metagenomics."' + EDAM operation: + - Taxonomic classification + - Expression analysis + - Cross-assembly + EDAM operation (no superclasses): + - Taxonomic classification + - Expression analysis + - Cross-assembly + EDAM topic: + - Metagenomics + - Microbial ecology + - Metagenomic sequencing + EDAM topic (no superclasses): + - Metagenomics + - Microbial ecology + - Metagenomic sequencing + Galaxy tool ids: + - recentrifuge + Galaxy wrapper id: recentrifuge + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge + Galaxy wrapper version: 1.15.0 + No. of tool users (5 years) (usegalaxy.eu): 472 + No. of tool users (5 years) (usegalaxy.org): 32 + No. of tool users (5 years) (usegalaxy.org.au): 6 + No. of tool users (5 years) - all main servers: 510 + No. of tool users (all time) (usegalaxy.eu): 472 + No. of tool users (all time) (usegalaxy.org): 32 + No. of tool users (all time) (usegalaxy.org.au): 6 + No. of tool users (all time) - all main servers: 510 + Source: https://github.com/khyox/recentrifuge + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 92 + Tool usage (5 years) (usegalaxy.org): 13 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 109 + Tool usage (all time) (usegalaxy.eu): 92 + Tool usage (all time) (usegalaxy.org): 13 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 109 + ToolShed categories: + - Metagenomics + ToolShed id: recentrifuge + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Robust comparative analysis and contamination removal for + metagenomics. + bio.tool id: Recentrifuge + bio.tool ids: + - Recentrifuge + bio.tool name: Recentrifuge +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: red + Conda version: 2018.09.10 + Date of first commit of the suite: '2022-09-14' + Description: Red (REpeat Detector) + EDAM operation: + - RNA-Seq analysis + - Editing + EDAM operation (no superclasses): + - RNA-Seq analysis + - Editing + EDAM topic: + - RNA + - Sequencing + - Data visualisation + EDAM topic (no superclasses): + - RNA + - Sequencing + - Data visualisation + Galaxy tool ids: + - red + Galaxy wrapper id: red + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/red + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/red + Galaxy wrapper version: 2018.09.10 + No. of tool users (5 years) (usegalaxy.eu): 859 + No. of tool users (5 years) (usegalaxy.org): 305 + No. of tool users (5 years) (usegalaxy.org.au): 227 + No. of tool users (5 years) - all main servers: 1391 + No. of tool users (all time) (usegalaxy.eu): 859 + No. of tool users (all time) (usegalaxy.org): 305 + No. of tool users (all time) (usegalaxy.org.au): 227 + No. of tool users (all time) - all main servers: 1391 + Source: https://github.com/BioinformaticsToolsmith/Red + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 203 + Tool usage (5 years) (usegalaxy.org): 142 + Tool usage (5 years) (usegalaxy.org.au): 58 + Tool usage (5 years) - all main servers: 403 + Tool usage (all time) (usegalaxy.eu): 203 + Tool usage (all time) (usegalaxy.org): 142 + Tool usage (all time) (usegalaxy.org.au): 58 + Tool usage (all time) - all main servers: 403 + ToolShed categories: + - Sequence Analysis + ToolShed id: red + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This is a program to detect and visualize RNA editing events + at genomic scale using next-generation sequencing data. + bio.tool id: red + bio.tool ids: + - red + bio.tool name: RED +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: repeatmasker + Conda version: 4.0.9_p2 + Date of first commit of the suite: '2018-04-30' + Description: RepeatMasker is a program that screens DNA sequences for interspersed + repeats and low complexity DNA sequences. + EDAM operation: + - Genome annotation + EDAM operation (no superclasses): + - Genome annotation + EDAM topic: + - Sequence analysis + - Sequence composition, complexity and repeats + EDAM topic (no superclasses): + - Sequence composition, complexity and repeats + Galaxy tool ids: + - repeatmasker_wrapper + Galaxy wrapper id: repeatmasker + Galaxy wrapper owner: bgruening + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker + Galaxy wrapper version: 4.1.5 + No. of tool users (5 years) (usegalaxy.eu): 5998 + No. of tool users (5 years) (usegalaxy.org): 7618 + No. of tool users (5 years) (usegalaxy.org.au): 3135 + No. of tool users (5 years) - all main servers: 16751 + No. of tool users (all time) (usegalaxy.eu): 5998 + No. of tool users (all time) (usegalaxy.org): 7618 + No. of tool users (all time) (usegalaxy.org.au): 3135 + No. of tool users (all time) - all main servers: 16751 + Source: http://www.repeatmasker.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 810 + Tool usage (5 years) (usegalaxy.org): 803 + Tool usage (5 years) (usegalaxy.org.au): 292 + Tool usage (5 years) - all main servers: 1905 + Tool usage (all time) (usegalaxy.eu): 810 + Tool usage (all time) (usegalaxy.org): 803 + Tool usage (all time) (usegalaxy.org.au): 292 + Tool usage (all time) - all main servers: 1905 + ToolShed categories: + - Sequence Analysis + ToolShed id: repeat_masker + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'A program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences. The output of the program is a detailed annotation + of the repeats that are present in the query sequence as well as a modified version + of the query sequence in which all the annotated repeats have been masked (default: + replaced by Ns).' + bio.tool id: repeatmasker + bio.tool ids: + - repeatmasker + bio.tool name: RepeatMasker +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-08-26' + Description: RepeatModeler - Model repetitive DNA + EDAM operation: + - Repeat sequence detection + EDAM operation (no superclasses): + - Repeat sequence detection + EDAM topic: + - Sequence composition, complexity and repeats + - Sequence composition, complexity and repeats + EDAM topic (no superclasses): + - Sequence composition, complexity and repeats + - Sequence composition, complexity and repeats + Galaxy tool ids: + - repeatmodeler + Galaxy wrapper id: repeatmodeler + Galaxy wrapper owner: csbl + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler + Galaxy wrapper version: 2.0.5 + No. of tool users (5 years) (usegalaxy.eu): 7963 + No. of tool users (5 years) (usegalaxy.org): 1485 + No. of tool users (5 years) (usegalaxy.org.au): 8402 + No. of tool users (5 years) - all main servers: 17850 + No. of tool users (all time) (usegalaxy.eu): 7963 + No. of tool users (all time) (usegalaxy.org): 1485 + No. of tool users (all time) (usegalaxy.org.au): 8402 + No. of tool users (all time) - all main servers: 17850 + Source: https://www.repeatmasker.org/RepeatModeler/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 413 + Tool usage (5 years) (usegalaxy.org): 220 + Tool usage (5 years) (usegalaxy.org.au): 168 + Tool usage (5 years) - all main servers: 801 + Tool usage (all time) (usegalaxy.eu): 413 + Tool usage (all time) (usegalaxy.org): 220 + Tool usage (all time) (usegalaxy.org.au): 168 + Tool usage (all time) - all main servers: 801 + ToolShed categories: + - Genome annotation + ToolShed id: repeatmodeler + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: De-novo repeat family identification and modeling package. + At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON + and RepeatScout ) which employ complementary computational methods for identifying + repeat element boundaries and family relationships from sequence data. RepeatModeler + assists in automating the runs of RECON and RepeatScout given a genomic database + and uses the output to build, refine and classify consensus models of putative + interspersed repeats. + bio.tool id: repeatmodeler + bio.tool ids: + - repeatmodeler + bio.tool name: RepeatModeler +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: matplotlib + Conda version: null + Date of first commit of the suite: '2015-12-18' + Description: Contains a tool that matches corresponding peak-pair midpoints from + separate datasets based onuser-defined criteria. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - repmatch_gff3 + Galaxy wrapper id: repmatch_gff3 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 415 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 415 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 721 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 721 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 128 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 128 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 219 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 219 + ToolShed categories: + - ChIP-seq + ToolShed id: repmatch_gff3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: r-reshape2 + Conda version: null + Date of first commit of the suite: '2017-05-26' + Description: Flexibly restructure and aggregate data using just the two functions + melt and dcast + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cast + - melt + Galaxy wrapper id: reshape2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 + Galaxy wrapper version: 1.4.2 + No. of tool users (5 years) (usegalaxy.eu): 3543 + No. of tool users (5 years) (usegalaxy.org): 536 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4079 + No. of tool users (all time) (usegalaxy.eu): 3619 + No. of tool users (all time) (usegalaxy.org): 536 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4155 + Source: https://cran.r-project.org/web/packages/reshape2/index.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 108 + Tool usage (5 years) (usegalaxy.org): 157 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 265 + Tool usage (all time) (usegalaxy.eu): 111 + Tool usage (all time) (usegalaxy.org): 157 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 268 + ToolShed categories: + - Text Manipulation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2016-01-13' + Description: Contains a tool that modifies the start and stop coordinates of GFF + data, expanding the coordinate windowby a specified size. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - resize_coordinate_window + Galaxy wrapper id: resize_coordinate_window + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 75 + No. of tool users (5 years) (usegalaxy.org): 138 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 213 + No. of tool users (all time) (usegalaxy.eu): 86 + No. of tool users (all time) (usegalaxy.org): 216 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 302 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 30 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 38 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 57 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 66 + ToolShed categories: + - Genomic Interval Operations + ToolShed id: resize_coordinate_window + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: revoluzer + Conda version: 0.1.6 + Date of first commit of the suite: '2024-03-19' + Description: revoluzer wrappers + EDAM operation: + - Structural variation detection + EDAM operation (no superclasses): + - Structural variation detection + EDAM topic: + - Molecular evolution + - Phylogeny + EDAM topic (no superclasses): + - Molecular evolution + - Phylogeny + Galaxy tool ids: + - revoluzer_crex + - revoluzer_distmat + Galaxy wrapper id: revoluzer + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer + Galaxy wrapper version: 0.1.6 + No. of tool users (5 years) (usegalaxy.eu): 2444 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2444 + No. of tool users (all time) (usegalaxy.eu): 2444 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2444 + Source: https://gitlab.com/Bernt/revoluzer/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 52 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 52 + Tool usage (all time) (usegalaxy.eu): 52 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 52 + ToolShed categories: + - Phylogenetics + ToolShed id: revoluzer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + biii: null + bio.tool description: Various tools for genome rearrangement analysis. CREx, TreeREx, + etc + bio.tool id: revoluzer + bio.tool ids: + - revoluzer + bio.tool name: revoluzer +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: rgccacmd + Conda version: 3.0.3 + Date of first commit of the suite: '2020-09-02' + Description: multi-block analysis + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rgcca + Galaxy wrapper id: rgcca + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca + Galaxy wrapper version: 3.0.2 + No. of tool users (5 years) (usegalaxy.eu): 44 + No. of tool users (5 years) (usegalaxy.org): 77 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 121 + No. of tool users (all time) (usegalaxy.eu): 44 + No. of tool users (all time) (usegalaxy.org): 77 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 121 + Source: https://github.com/rgcca-factory/RGCCA + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 35 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 41 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 35 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 41 + ToolShed categories: + - Statistics + ToolShed id: rgcca + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: star + Conda version: 2.7.11b + Date of first commit of the suite: '2023-02-27' + Description: RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper + EDAM operation: + - Sequence alignment + EDAM operation (no superclasses): + - Sequence alignment + EDAM topic: + - RNA-Seq + - Transcriptomics + EDAM topic (no superclasses): + - RNA-Seq + - Transcriptomics + Galaxy tool ids: + - rna_star + - rna_starsolo + Galaxy wrapper id: rgrnastar + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar + Galaxy wrapper version: 2.7.11a + No. of tool users (5 years) (usegalaxy.eu): 438078 + No. of tool users (5 years) (usegalaxy.org): 325474 + No. of tool users (5 years) (usegalaxy.org.au): 49662 + No. of tool users (5 years) - all main servers: 813214 + No. of tool users (all time) (usegalaxy.eu): 473957 + No. of tool users (all time) (usegalaxy.org): 403925 + No. of tool users (all time) (usegalaxy.org.au): 53138 + No. of tool users (all time) - all main servers: 931020 + Source: https://github.com/alexdobin/STAR + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10142 + Tool usage (5 years) (usegalaxy.org): 15284 + Tool usage (5 years) (usegalaxy.org.au): 1359 + Tool usage (5 years) - all main servers: 26785 + Tool usage (all time) (usegalaxy.eu): 10900 + Tool usage (all time) (usegalaxy.org): 18791 + Tool usage (all time) (usegalaxy.org.au): 1449 + Tool usage (all time) - all main servers: 31140 + ToolShed categories: + - Next Gen Mappers + - Transcriptomics + ToolShed id: rgrnastar + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 2 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Ultrafast universal RNA-seq data aligner + bio.tool id: star + bio.tool ids: + - star + bio.tool name: STAR +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ribowaltz + Conda version: '2.0' + Date of first commit of the suite: '2022-09-22' + Description: Calculation of optimal P-site offsets, diagnostic analysis and visual + inspection of ribosome profiling data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Computational biology + EDAM topic (no superclasses): + - Computational biology + Galaxy tool ids: + - ribowaltz_process + - ribowaltz_plot + Galaxy wrapper id: ribowaltz + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 171 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 171 + No. of tool users (all time) (usegalaxy.eu): 171 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 171 + Source: https://github.com/LabTranslationalArchitectomics/riboWaltz + Status: To update + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 20 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 20 + ToolShed categories: + - Transcriptomics + - RNA + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + biii: null + bio.tool description: riboWaltz is an R package for calculation of optimal P-site + offsets, diagnostic analysis and visual inspection of ribosome profiling data. + bio.tool id: riboWaltz + bio.tool ids: + - riboWaltz + bio.tool name: riboWaltz +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: rnaquast + Conda version: 2.3.0 + Date of first commit of the suite: '2023-06-03' + Description: rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. + EDAM operation: + - De-novo assembly + - Transcriptome assembly + - Sequence assembly validation + EDAM operation (no superclasses): + - De-novo assembly + - Transcriptome assembly + - Sequence assembly validation + EDAM topic: + - Sequence assembly + - Transcriptomics + - RNA-seq + EDAM topic (no superclasses): + - Sequence assembly + - Transcriptomics + Galaxy tool ids: + - rna_quast + Galaxy wrapper id: rnaquast + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast + Galaxy wrapper source: https://git.ufz.de/lehmanju/rnaquast + Galaxy wrapper version: 2.3.0 + No. of tool users (5 years) (usegalaxy.eu): 1522 + No. of tool users (5 years) (usegalaxy.org): 372 + No. of tool users (5 years) (usegalaxy.org.au): 5 + No. of tool users (5 years) - all main servers: 1899 + No. of tool users (all time) (usegalaxy.eu): 1522 + No. of tool users (all time) (usegalaxy.org): 372 + No. of tool users (all time) (usegalaxy.org.au): 5 + No. of tool users (all time) - all main servers: 1899 + Source: https://github.com/ablab/rnaquast + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 254 + Tool usage (5 years) (usegalaxy.org): 75 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 330 + Tool usage (all time) (usegalaxy.eu): 254 + Tool usage (all time) (usegalaxy.org): 75 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 330 + ToolShed categories: + - Assembly + - RNA + ToolShed id: rnaquast + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Quality assessment tool for de novo transcriptome assemblies. + bio.tool id: rnaQUAST + bio.tool ids: + - rnaQUAST + bio.tool name: rnaQUAST +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: roary + Conda version: 3.13.0 + Date of first commit of the suite: '2017-06-21' + Description: Roary the pangenome pipeline + EDAM operation: + - Genome assembly + EDAM operation (no superclasses): + - Genome assembly + EDAM topic: + - DNA + - Genomics + - Mapping + EDAM topic (no superclasses): + - DNA + - Genomics + - Mapping + Galaxy tool ids: + - roary + Galaxy wrapper id: roary + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary + Galaxy wrapper version: 3.13.0 + No. of tool users (5 years) (usegalaxy.eu): 15196 + No. of tool users (5 years) (usegalaxy.org): 12188 + No. of tool users (5 years) (usegalaxy.org.au): 4881 + No. of tool users (5 years) - all main servers: 32265 + No. of tool users (all time) (usegalaxy.eu): 15685 + No. of tool users (all time) (usegalaxy.org): 12188 + No. of tool users (all time) (usegalaxy.org.au): 5539 + No. of tool users (all time) - all main servers: 33412 + Source: https://sanger-pathogens.github.io/Roary/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1459 + Tool usage (5 years) (usegalaxy.org): 1768 + Tool usage (5 years) (usegalaxy.org.au): 518 + Tool usage (5 years) - all main servers: 3745 + Tool usage (all time) (usegalaxy.eu): 1501 + Tool usage (all time) (usegalaxy.org): 1768 + Tool usage (all time) (usegalaxy.org.au): 555 + Tool usage (all time) - all main servers: 3824 + ToolShed categories: + - Sequence Analysis + ToolShed id: roary + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A high speed stand alone pan genome pipeline, which takes + annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates + the pan genome. + bio.tool id: roary + bio.tool ids: + - roary + bio.tool name: Roary +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rp2biosensor + Conda version: null + Date of first commit of the suite: '2023-01-05' + Description: Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rp2biosensor + Galaxy wrapper id: rp2biosensor + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor + Galaxy wrapper version: 3.2.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/brsynth/rp2biosensor + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: rp2biosensor + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rp2paths + Conda version: null + Date of first commit of the suite: '2022-10-17' + Description: Enumerate and seperate the different pathways generated by RetroPath2.0 + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rp2paths + Galaxy wrapper id: rp2paths + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths + Galaxy wrapper version: 1.5.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/brsynth/rp2paths + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: rp2paths + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rpbasicdesign + Conda version: null + Date of first commit of the suite: '2022-03-30' + Description: Extracting enzyme IDs from rpSBML files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rpbasicdesign + Galaxy wrapper id: rpbasicdesign + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign + Galaxy wrapper version: 1.2.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/brsynth/rpbasicdesign + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: rpbasicdesign + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rptools + Conda version: null + Date of first commit of the suite: '2022-01-17' + Description: Perform FBA for the RetroPath2.0 heterologous pathways + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rpfba + Galaxy wrapper id: rpfba + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba + Galaxy wrapper version: 5.12.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/brsynth/rptools/releases + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: rpfba + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rptools + Conda version: null + Date of first commit of the suite: '2022-11-16' + Description: Suite of tools that work on rpSBML format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rptools_rpextractsink + - rptools_rpfba + - rptools_rpranker + - rptools_rpreport + - rptools_rpviz + Galaxy wrapper id: rptools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools + Galaxy wrapper version: 5.13.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/brsynth/rptools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: rptools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rrparser + Conda version: null + Date of first commit of the suite: '2022-06-27' + Description: Reaction Rules Parser + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rrparser + Galaxy wrapper id: rrparser + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser + Galaxy wrapper version: 2.5.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/brsynth/RRParser + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: rrparser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 22 + Available on UseGalaxy.fr: 22 + Available on UseGalaxy.org (Main): 22 + Available on UseGalaxy.org.au: 22 + Conda id: rseqc + Conda version: 5.0.4 + Date of first commit of the suite: '2017-02-27' + Description: an RNA-seq quality control package + EDAM operation: + - Data handling + EDAM operation (no superclasses): + - Data handling + EDAM topic: + - Sequencing + EDAM topic (no superclasses): + - Sequencing + Galaxy tool ids: + - rseqc_FPKM_count + - rseqc_RNA_fragment_size + - rseqc_RPKM_saturation + - rseqc_bam2wig + - rseqc_bam_stat + - rseqc_clipping_profile + - rseqc_deletion_profile + - rseqc_geneBody_coverage + - rseqc_geneBody_coverage2 + - rseqc_infer_experiment + - rseqc_inner_distance + - rseqc_insertion_profile + - rseqc_junction_annotation + - rseqc_junction_saturation + - rseqc_mismatch_profile + - rseqc_read_GC + - rseqc_read_NVC + - rseqc_read_distribution + - rseqc_read_duplication + - rseqc_read_hexamer + - rseqc_read_quality + - rseqc_tin + Galaxy wrapper id: rseqc + Galaxy wrapper owner: nilesh + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc + Galaxy wrapper version: 5.0.3 + No. of tool users (5 years) (usegalaxy.eu): 136315 + No. of tool users (5 years) (usegalaxy.org): 138707 + No. of tool users (5 years) (usegalaxy.org.au): 22718 + No. of tool users (5 years) - all main servers: 297740 + No. of tool users (all time) (usegalaxy.eu): 147595 + No. of tool users (all time) (usegalaxy.org): 161046 + No. of tool users (all time) (usegalaxy.org.au): 23767 + No. of tool users (all time) - all main servers: 332408 + Source: https://code.google.com/p/rseqc/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8341 + Tool usage (5 years) (usegalaxy.org): 10696 + Tool usage (5 years) (usegalaxy.org.au): 1593 + Tool usage (5 years) - all main servers: 20630 + Tool usage (all time) (usegalaxy.eu): 9385 + Tool usage (all time) (usegalaxy.org): 12789 + Tool usage (all time) (usegalaxy.org.au): 1695 + Tool usage (all time) - all main servers: 23869 + ToolShed categories: + - Convert Formats + - Sequence Analysis + - RNA + - Transcriptomics + - Visualization + ToolShed id: rseqc + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 22 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 22 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 22 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 22 + Tools available on UseGalaxy.cz: 22 + Tools available on UseGalaxy.eu: 22 + Tools available on UseGalaxy.fr: 22 + Tools available on UseGalaxy.no: 22 + Tools available on UseGalaxy.org (Main): 22 + Tools available on UseGalaxy.org.au: 22 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 22 + UseGalaxy.cz: 22 + UseGalaxy.eu: 22 + UseGalaxy.fr: 22 + UseGalaxy.no: 22 + UseGalaxy.or: 22 + biii: null + bio.tool description: Provides a number of useful modules that can comprehensively + evaluate high throughput sequence data especially RNA-seq data. Some basic modules + quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC + bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads + distribution, coverage uniformity, strand specificity, transcript level RNA integrity + etc. + bio.tool id: rseqc + bio.tool ids: + - rseqc + bio.tool name: RSeQC +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-ruvseq + Conda version: 1.36.0 + Date of first commit of the suite: '2018-08-30' + Description: Remove Unwanted Variation from RNA-Seq Data + EDAM operation: + - Differential gene expression analysis + EDAM operation (no superclasses): + - Differential gene expression analysis + EDAM topic: + - Gene expression + - RNA-seq + EDAM topic (no superclasses): + - Gene expression + Galaxy tool ids: + - ruvseq + Galaxy wrapper id: ruvseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq + Galaxy wrapper version: 1.26.0 + No. of tool users (5 years) (usegalaxy.eu): 1286 + No. of tool users (5 years) (usegalaxy.org): 2220 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3506 + No. of tool users (all time) (usegalaxy.eu): 1364 + No. of tool users (all time) (usegalaxy.org): 2220 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3584 + Source: https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 178 + Tool usage (5 years) (usegalaxy.org): 299 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 477 + Tool usage (all time) (usegalaxy.eu): 193 + Tool usage (all time) (usegalaxy.org): 299 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 492 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: ruvseq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This package implements the remove unwanted variation (RUV) + methods for the normalization of RNA-Seq read counts between samples. + bio.tool id: ruvseq + bio.tool ids: + - ruvseq + bio.tool name: RUVSeq +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: salsa2 + Conda version: '2.3' + Date of first commit of the suite: '2021-01-14' + Description: A tool to scaffold long read assemblies with Hi-C + EDAM operation: + - Genome assembly + - De-novo assembly + - Scaffolding + EDAM operation (no superclasses): + - Genome assembly + - De-novo assembly + - Scaffolding + EDAM topic: + - Sequence assembly + - DNA binding sites + - Mapping + EDAM topic (no superclasses): + - Sequence assembly + - DNA binding sites + - Mapping + Galaxy tool ids: + - salsa + Galaxy wrapper id: salsa2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 + Galaxy wrapper version: '2.3' + No. of tool users (5 years) (usegalaxy.eu): 463 + No. of tool users (5 years) (usegalaxy.org): 1038 + No. of tool users (5 years) (usegalaxy.org.au): 410 + No. of tool users (5 years) - all main servers: 1911 + No. of tool users (all time) (usegalaxy.eu): 463 + No. of tool users (all time) (usegalaxy.org): 1038 + No. of tool users (all time) (usegalaxy.org.au): 410 + No. of tool users (all time) - all main servers: 1911 + Source: https://github.com/marbl/SALSA + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 119 + Tool usage (5 years) (usegalaxy.org): 87 + Tool usage (5 years) (usegalaxy.org.au): 24 + Tool usage (5 years) - all main servers: 230 + Tool usage (all time) (usegalaxy.eu): 119 + Tool usage (all time) (usegalaxy.org): 87 + Tool usage (all time) (usegalaxy.org.au): 24 + Tool usage (all time) - all main servers: 230 + ToolShed categories: + - Assembly + ToolShed id: salsa + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: '> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO + BE ''chromosome-scale'', ''reference-quality'', ''Hi-C'', ''scaffolder'' | Integrating + Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool + to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long + read assemblies with Hi-C | This code is used to scaffold your assemblies using + Hi-C data. This version implements some improvements in the original SALSA algorithm. + If you want to use the old version, it can be found in the old_salsa branch' + bio.tool id: SALSA + bio.tool ids: + - SALSA + bio.tool name: SALSA +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: samblaster + Conda version: 0.1.26 + Date of first commit of the suite: '2016-12-18' + Description: samblaster marks duplicates and can output split and discordant alignments + from SAM/BAM files + EDAM operation: + - Split read mapping + EDAM operation (no superclasses): + - Split read mapping + EDAM topic: + - DNA + - Sequencing + - Mapping + EDAM topic (no superclasses): + - DNA + - Sequencing + - Mapping + Galaxy tool ids: + - samblaster + Galaxy wrapper id: samblaster + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster + Galaxy wrapper version: 0.1.26 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/GregoryFaust/samblaster + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - SAM + - Fastq Manipulation + - Variant Analysis + ToolShed id: samblaster + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: A tool to mark duplicates and extract discordant and split + reads from SAM files. + bio.tool id: samblaster + bio.tool ids: + - samblaster + bio.tool name: SAMBLASTER +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: sansa + Conda version: 0.2.2 + Date of first commit of the suite: '2020-12-05' + Description: Sansa is a tool for structural variant annotation. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sansa_annotate + Galaxy wrapper id: sansa + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa + Galaxy wrapper version: 0.2.2 + No. of tool users (5 years) (usegalaxy.eu): 138 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 138 + No. of tool users (all time) (usegalaxy.eu): 138 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 138 + Source: https://github.com/dellytools/sansa + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 36 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 36 + Tool usage (all time) (usegalaxy.eu): 36 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 36 + ToolShed categories: + - Variant Analysis + ToolShed id: sansa + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: sarscov2formatter + Conda version: '1.0' + Date of first commit of the suite: '2020-05-01' + Description: sarscov2formatter custom script + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sarscov2formatter + Galaxy wrapper id: sarscov2formatter + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 174 + No. of tool users (5 years) (usegalaxy.org): 399 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 573 + No. of tool users (all time) (usegalaxy.eu): 174 + No. of tool users (all time) (usegalaxy.org): 399 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 573 + Source: https://github.com/nickeener/sarscov2formatter + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 29 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 45 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 29 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 45 + ToolShed categories: + - Sequence Analysis + ToolShed id: sarscov2formatter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: sarscov2summary + Conda version: '0.5' + Date of first commit of the suite: '2020-05-01' + Description: sarscov2summary custom script + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sarscov2summary + Galaxy wrapper id: sarscov2summary + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 140 + No. of tool users (5 years) (usegalaxy.org): 253 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 393 + No. of tool users (all time) (usegalaxy.eu): 140 + No. of tool users (all time) (usegalaxy.org): 253 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 393 + Source: https://github.com/nickeener/sarscov2summary + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 6 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 6 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Sequence Analysis + ToolShed id: sarscov2summary + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: sbml2sbol + Conda version: null + Date of first commit of the suite: '2022-10-15' + Description: Convert SBML to SBOL format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sbml2sbol + Galaxy wrapper id: sbml2sbol + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol + Galaxy wrapper version: 0.1.13 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/neilswainston/SbmlToSbol + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: sbml2sbol + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 6 + Available on UseGalaxy.org.au: 6 + Conda id: scanpy + Conda version: 1.7.2 + Date of first commit of the suite: '2024-09-03' + Description: "Scanpy \u2013 Single-Cell Analysis in Python" + EDAM operation: + - Differential gene expression analysis + EDAM operation (no superclasses): + - Differential gene expression analysis + EDAM topic: + - Gene expression + - Cell biology + - Genetics + EDAM topic (no superclasses): + - Gene expression + - Cell biology + - Genetics + Galaxy tool ids: + - scanpy_cluster_reduce_dimension + - scanpy_filter + - scanpy_inspect + - scanpy_normalize + - scanpy_plot + - scanpy_remove_confounders + Galaxy wrapper id: scanpy + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ + Galaxy wrapper version: 1.10.2 + No. of tool users (5 years) (usegalaxy.eu): 63789 + No. of tool users (5 years) (usegalaxy.org): 29962 + No. of tool users (5 years) (usegalaxy.org.au): 18028 + No. of tool users (5 years) - all main servers: 111779 + No. of tool users (all time) (usegalaxy.eu): 64034 + No. of tool users (all time) (usegalaxy.org): 29962 + No. of tool users (all time) (usegalaxy.org.au): 18028 + No. of tool users (all time) - all main servers: 112024 + Source: https://scanpy.readthedocs.io + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2543 + Tool usage (5 years) (usegalaxy.org): 1185 + Tool usage (5 years) (usegalaxy.org.au): 379 + Tool usage (5 years) - all main servers: 4107 + Tool usage (all time) (usegalaxy.eu): 2547 + Tool usage (all time) (usegalaxy.org): 1185 + Tool usage (all time) (usegalaxy.org.au): 379 + Tool usage (all time) - all main servers: 4111 + ToolShed categories: + - Single Cell + - Spatial Omics + - Transcriptomics + ToolShed id: scanpy + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 6 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 6 + Tools available on UseGalaxy.org (Main): 6 + Tools available on UseGalaxy.org.au: 6 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 6 + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.no: 6 + UseGalaxy.or: 6 + biii: null + bio.tool description: Scalable toolkit for analyzing single-cell gene expression + data. It includes preprocessing, visualization, clustering, pseudotime and trajectory + inference and differential expression testing. The Python-based implementation + efficiently deals with datasets of more than one million cells. + bio.tool id: scanpy + bio.tool ids: + - scanpy + bio.tool name: SCANPY +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 5 + Conda id: bioconductor-scater + Conda version: 1.30.1 + Date of first commit of the suite: '2019-07-18' + Description: Scater (Single-Cell Analysis Toolkit for gene Expression data in R) + is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression + data, with a focus on quality control and visualization. + EDAM operation: + - Read pre-processing + - Sequencing quality control + - Sequence visualisation + EDAM operation (no superclasses): + - Read pre-processing + - Sequence visualisation + EDAM topic: + - RNA-seq + - Quality affairs + - Molecular genetics + EDAM topic (no superclasses): + - Quality affairs + - Molecular genetics + Galaxy tool ids: + - scater_create_qcmetric_ready_sce + - scater_filter + - scater_plot_dist_scatter + - scater_plot_pca + - scater_plot_tsne + Galaxy wrapper id: scater + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater + Galaxy wrapper version: 1.22.0 + No. of tool users (5 years) (usegalaxy.eu): 1345 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 903 + No. of tool users (5 years) - all main servers: 2248 + No. of tool users (all time) (usegalaxy.eu): 1371 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 903 + No. of tool users (all time) - all main servers: 2274 + Source: http://bioconductor.org/packages/scater/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 350 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 29 + Tool usage (5 years) - all main servers: 379 + Tool usage (all time) (usegalaxy.eu): 351 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 29 + Tool usage (all time) - all main servers: 380 + ToolShed categories: + - Single Cell + - Transcriptomics + - Visualization + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: Pre-processing, quality control, normalization and visualization + of single-cell RNA-seq data. + bio.tool id: scater + bio.tool ids: + - scater + bio.tool name: scater +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-sceasy + Conda version: 0.0.7 + Date of first commit of the suite: '2023-11-10' + Description: Converter between difference single-cell formats + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sceasy_convert + Galaxy wrapper id: sceasy + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ + Galaxy wrapper version: 0.0.7 + No. of tool users (5 years) (usegalaxy.eu): 1059 + No. of tool users (5 years) (usegalaxy.org): 426 + No. of tool users (5 years) (usegalaxy.org.au): 1 + No. of tool users (5 years) - all main servers: 1486 + No. of tool users (all time) (usegalaxy.eu): 1059 + No. of tool users (all time) (usegalaxy.org): 426 + No. of tool users (all time) (usegalaxy.org.au): 1 + No. of tool users (all time) - all main servers: 1486 + Source: https://github.com/cellgeni/sceasy/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 222 + Tool usage (5 years) (usegalaxy.org): 71 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 294 + Tool usage (all time) (usegalaxy.eu): 222 + Tool usage (all time) (usegalaxy.org): 71 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 294 + ToolShed categories: + - Single Cell + - Spatial Omics + - Convert Formats + ToolShed id: sceasy_convert + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 16 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 16 + Available on UseGalaxy.org.au: 16 + Conda id: schicexplorer + Conda version: '7' + Date of first commit of the suite: '2019-12-16' + Description: 'scHiCExplorer: Set of programs to process, analyze and visualize scHi-C + data.' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - schicexplorer_schicadjustmatrix + - schicexplorer_schiccluster + - schicexplorer_schicclustercompartments + - schicexplorer_schicclusterminhash + - schicexplorer_schicclustersvl + - schicexplorer_schicconsensusmatrices + - schicexplorer_schiccorrectmatrices + - schicexplorer_schiccreatebulkmatrix + - schicexplorer_schicdemultiplex + - schicexplorer_schicinfo + - schicexplorer_schicmergematrixbins + - schicexplorer_schicmergetoscool + - schicexplorer_schicnormalize + - schicexplorer_schicplotclusterprofiles + - schicexplorer_schicplotconsensusmatrices + - schicexplorer_schicqualitycontrol + Galaxy wrapper id: schicexplorer + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer + Galaxy wrapper version: '4' + No. of tool users (5 years) (usegalaxy.eu): 809 + No. of tool users (5 years) (usegalaxy.org): 3 + No. of tool users (5 years) (usegalaxy.org.au): 105 + No. of tool users (5 years) - all main servers: 917 + No. of tool users (all time) (usegalaxy.eu): 809 + No. of tool users (all time) (usegalaxy.org): 3 + No. of tool users (all time) (usegalaxy.org.au): 105 + No. of tool users (all time) - all main servers: 917 + Source: https://github.com/joachimwolff/schicexplorer + Status: To update + Tool usage (5 years) (usegalaxy.eu): 78 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 16 + Tool usage (5 years) - all main servers: 96 + Tool usage (all time) (usegalaxy.eu): 78 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 16 + Tool usage (all time) - all main servers: 96 + ToolShed categories: + - Sequence Analysis + - Transcriptomics + - Visualization + - Single Cell + ToolShed id: schicexplorer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 16 + Tools available on UseGalaxy.cz: 16 + Tools available on UseGalaxy.eu: 16 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 16 + Tools available on UseGalaxy.org (Main): 16 + Tools available on UseGalaxy.org.au: 16 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 16 + UseGalaxy.cz: 16 + UseGalaxy.eu: 16 + UseGalaxy.no: 16 + UseGalaxy.or: 16 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: scikit-bio + Conda version: 0.4.2 + Date of first commit of the suite: '2016-05-31' + Description: 'scikit-bio: an open-source, BSD-licensed, python package providing + data structures, algorithms, and educational resources for bioinformatics' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - scikit_bio_diversity_beta_diversity + Galaxy wrapper id: scikit-bio + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio + Galaxy wrapper version: 0.4.2 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 1503 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1504 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 1955 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1956 + Source: http://scikit-bio.org/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 283 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 284 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 402 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 403 + ToolShed categories: + - Sequence Analysis + ToolShed id: scikit_bio + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scoary + Conda version: 1.6.16 + Date of first commit of the suite: '2021-03-18' + Description: Scoary calculates the assocations between all genes in the accessory + genome and the traits. + EDAM operation: + - Analysis + EDAM operation (no superclasses): + - Analysis + EDAM topic: + - Genotype and phenotype + - Model organisms + - GWAS study + - Functional genomics + EDAM topic (no superclasses): + - Genotype and phenotype + - Model organisms + - GWAS study + - Functional genomics + Galaxy tool ids: + - scoary + Galaxy wrapper id: scoary + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary + Galaxy wrapper version: 1.6.16 + No. of tool users (5 years) (usegalaxy.eu): 901 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 901 + No. of tool users (all time) (usegalaxy.eu): 901 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 901 + Source: https://github.com/AdmiralenOla/Scoary + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 90 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 90 + Tool usage (all time) (usegalaxy.eu): 90 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 90 + ToolShed categories: + - Metagenomics + ToolShed id: scoary + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Pan-genome wide association studies and is designed to take + the gene_presence_absence.csv file from Roary as well as a traits file created + by the user and calculate the assocations between all genes in the accessory genome + (all genes that are present in i genomes where 1 < i < N) and the traits. It reports + a list of genes sorted by strength of association per trait. + bio.tool id: scoary + bio.tool ids: + - scoary + bio.tool name: Scoary +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-scpipe + Conda version: 2.2.0 + Date of first commit of the suite: '2018-08-13' + Description: A flexible preprocessing pipeline for single-cell RNA-sequencing data + EDAM operation: + - Genome annotation + - Validation + - Alignment + - Visualisation + EDAM operation (no superclasses): + - Genome annotation + - Validation + - Alignment + - Visualisation + EDAM topic: + - Gene expression + - RNA-Seq + - Sequencing + EDAM topic (no superclasses): + - Gene expression + - RNA-Seq + Galaxy tool ids: + - scpipe + Galaxy wrapper id: scpipe + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe + Galaxy wrapper version: 1.0.0+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 284 + No. of tool users (5 years) (usegalaxy.org): 786 + No. of tool users (5 years) (usegalaxy.org.au): 1 + No. of tool users (5 years) - all main servers: 1071 + No. of tool users (all time) (usegalaxy.eu): 632 + No. of tool users (all time) (usegalaxy.org): 786 + No. of tool users (all time) (usegalaxy.org.au): 1 + No. of tool users (all time) - all main servers: 1419 + Source: http://bioconductor.org/packages/release/bioc/html/scPipe.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 34 + Tool usage (5 years) (usegalaxy.org): 61 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 96 + Tool usage (all time) (usegalaxy.eu): 38 + Tool usage (all time) (usegalaxy.org): 61 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 100 + ToolShed categories: + - Transcriptomics + - Single Cell + ToolShed id: scpipe + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A preprocessing pipeline for single cell RNA-seq data that + starts from the fastq files and produces a gene count matrix with associated quality + control information. It can process fastq data generated by CEL-seq, MARS-seq, + Drop-seq, Chromium 10x and SMART-seq protocols. + bio.tool id: scpipe + bio.tool ids: + - scpipe + bio.tool name: scPipe +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: seacr + Conda version: '1.3' + Date of first commit of the suite: '2020-02-05' + Description: SEACR is intended to call peaks and enriched regions from sparse CUT&RUN + or chromatin profiling data in which background is dominated by zeroes. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - seacr + Galaxy wrapper id: seacr + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr + Galaxy wrapper version: '1.3' + No. of tool users (5 years) (usegalaxy.eu): 5106 + No. of tool users (5 years) (usegalaxy.org): 6419 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 11525 + No. of tool users (all time) (usegalaxy.eu): 5106 + No. of tool users (all time) (usegalaxy.org): 6419 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 11525 + Source: https://github.com/FredHutch/SEACR + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 116 + Tool usage (5 years) (usegalaxy.org): 241 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 357 + Tool usage (all time) (usegalaxy.eu): 116 + Tool usage (all time) (usegalaxy.org): 241 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 357 + ToolShed categories: + - Epigenetics + - ChIP-seq + ToolShed id: seacr + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: selenzy_wrapper + Conda version: 0.3.0 + Date of first commit of the suite: '2022-06-29' + Description: Performs enzyme selection from a reaction query. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - selenzy_wrapper + Galaxy wrapper id: selenzy_wrapper + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper + Galaxy wrapper version: 0.3.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/brsynth/selenzy-wrapper + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Synthetic Biology + ToolShed id: selenzy_wrapper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: semibin + Conda version: 2.1.0 + Date of first commit of the suite: '2022-10-14' + Description: 'SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural + Networks' + EDAM operation: + - Sequence assembly + - Read binning + EDAM operation (no superclasses): + - Sequence assembly + - Read binning + EDAM topic: + - Metagenomics + - Machine learning + - Microbial ecology + - Sequence assembly + EDAM topic (no superclasses): + - Metagenomics + - Machine learning + - Microbial ecology + - Sequence assembly + Galaxy tool ids: + - semibin_bin + - semibin_concatenate_fasta + - semibin_generate_cannot_links + - semibin_generate_sequence_features + - semibin + - semibin_train + Galaxy wrapper id: semibin + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin + Galaxy wrapper version: 2.0.2 + No. of tool users (5 years) (usegalaxy.eu): 931 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 931 + No. of tool users (all time) (usegalaxy.eu): 931 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 931 + Source: https://semibin.readthedocs.io/en/latest/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 93 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 93 + Tool usage (all time) (usegalaxy.eu): 93 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 93 + ToolShed categories: + - Metagenomics + ToolShed id: semibin + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Command tool for metagenomic binning with semi-supervised + deep learning using information from reference genomes. + bio.tool id: semibin + bio.tool ids: + - semibin + bio.tool name: SemiBin +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: seq2hla + Conda version: '2.3' + Date of first commit of the suite: '2020-02-20' + Description: Precision HLA typing and expression from RNAseq data + EDAM operation: + - Read mapping + - Genetic variation analysis + EDAM operation (no superclasses): + - Read mapping + - Genetic variation analysis + EDAM topic: + - Transcriptomics + - Mapping + EDAM topic (no superclasses): + - Transcriptomics + - Mapping + Galaxy tool ids: + - seq2hla + Galaxy wrapper id: seq2hla + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla + Galaxy wrapper version: '2.3' + No. of tool users (5 years) (usegalaxy.eu): 342 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 342 + No. of tool users (all time) (usegalaxy.eu): 342 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 342 + Source: https://github.com/TRON-Bioinformatics/seq2HLA + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 40 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 40 + Tool usage (all time) (usegalaxy.eu): 40 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 40 + ToolShed categories: + - Sequence Analysis + ToolShed id: seq2hla + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: seq2HLA is a computational tool to determine Human Leukocyte + Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes + standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index + comprising known HLA alleles and outputs the most likely HLA class I and class + II types, a p-value for each call, and the expression of each class. + bio.tool id: seq2hla + bio.tool ids: + - seq2hla + bio.tool name: Seq2HLA +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: seqcomplexity + Conda version: 0.1.2 + Date of first commit of the suite: '2022-06-07' + Description: Sequence complexity for raw reads + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - seqcomplexity + Galaxy wrapper id: seqcomplexity + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity + Galaxy wrapper source: https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 70 + No. of tool users (5 years) (usegalaxy.org): 109 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 179 + No. of tool users (all time) (usegalaxy.eu): 70 + No. of tool users (all time) (usegalaxy.org): 109 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 179 + Source: https://github.com/stevenweaver/seqcomplexity + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 19 + Tool usage (5 years) (usegalaxy.org): 47 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 66 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 47 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 66 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 2 + Conda id: seqkit + Conda version: 2.8.2 + Date of first commit of the suite: '2022-06-01' + Description: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation + EDAM operation: + - DNA transcription + - Sequence trimming + - DNA translation + - Sequence conversion + EDAM operation (no superclasses): + - DNA transcription + - Sequence trimming + - DNA translation + EDAM topic: + - Database management + - Sequence analysis + EDAM topic (no superclasses): + - Database management + - Sequence analysis + Galaxy tool ids: + - seqkit_fx2tab + - seqkit_locate + - seqkit_sort + - seqkit_stats + - seqkit_translate + Galaxy wrapper id: seqkit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit + Galaxy wrapper version: 2.8.2 + No. of tool users (5 years) (usegalaxy.eu): 3364 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 244 + No. of tool users (5 years) - all main servers: 3608 + No. of tool users (all time) (usegalaxy.eu): 3364 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 244 + No. of tool users (all time) - all main servers: 3608 + Source: https://bioinf.shenwei.me/seqkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 247 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 33 + Tool usage (5 years) - all main servers: 280 + Tool usage (all time) (usegalaxy.eu): 247 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 33 + Tool usage (all time) - all main servers: 280 + ToolShed categories: + - Sequence Analysis + ToolShed id: seqkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 5 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.or: 2 + biii: null + bio.tool description: FASTA and FASTQ are basic and ubiquitous formats for storing + nucleotide and protein sequences. Common manipulations of FASTA/Q file include + converting, searching, filtering, deduplication, splitting, shuffling, and sampling. + Existing tools only implement some of these manipulations, and not particularly + efficiently, and some are only available for certain operating systems. Furthermore, + the complicated installation process of required packages and running environments + can render these programs less user friendly. SeqKit demonstrates competitive + performance in execution time and memory usage compared to similar tools. The + efficiency and usability of SeqKit enable researchers to rapidly accomplish common + FASTA/Q file manipulations. + bio.tool id: seqkit + bio.tool ids: + - seqkit + bio.tool name: seqkit +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: seqprep + Conda version: 1.3.2 + Date of first commit of the suite: '2024-01-15' + Description: Tool for merging paired-end Illumina reads and trimming adapters. + EDAM operation: + - Nucleic acid design + EDAM operation (no superclasses): + - Nucleic acid design + EDAM topic: + - Genomics + - Sequence assembly + - Sequencing + - Probes and primers + EDAM topic (no superclasses): + - Genomics + - Sequence assembly + - Sequencing + - Probes and primers + Galaxy tool ids: + - seqprep + Galaxy wrapper id: seqprep + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep + Galaxy wrapper version: 1.3.2 + No. of tool users (5 years) (usegalaxy.eu): 2424 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2424 + No. of tool users (all time) (usegalaxy.eu): 2424 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2424 + Source: https://github.com/jstjohn/SeqPrep + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 102 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 102 + Tool usage (all time) (usegalaxy.eu): 102 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 102 + ToolShed categories: + - Fastq Manipulation + - Sequence Analysis + ToolShed id: seqprep + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Strips adapters and optionally merges overlapping paired-end + (or paired-end contamination in mate-pair libraries) illumina style reads. + bio.tool id: seqprep + bio.tool ids: + - seqprep + bio.tool name: SeqPrep +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: seqsero2 + Conda version: 1.3.1 + Date of first commit of the suite: '2023-11-07' + Description: Salmonella serotype prediction from genome sequencing data + EDAM operation: + - Genome indexing + - Antimicrobial resistance prediction + - Genome alignment + EDAM operation (no superclasses): + - Genome indexing + - Antimicrobial resistance prediction + - Genome alignment + EDAM topic: + - Whole genome sequencing + - Sequence assembly + - Genomics + EDAM topic (no superclasses): + - Whole genome sequencing + - Sequence assembly + - Genomics + Galaxy tool ids: + - seqsero2 + Galaxy wrapper id: seqsero2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 + Galaxy wrapper version: 1.3.1 + No. of tool users (5 years) (usegalaxy.eu): 4182 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4182 + No. of tool users (all time) (usegalaxy.eu): 4182 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4182 + Source: https://github.com/denglab/SeqSero2 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 42 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 42 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 42 + ToolShed categories: + - Sequence Analysis + ToolShed id: seqsero2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: 'rapid and improved Salmonella serotype determination using + whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing + | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 + | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, + Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants + databases | Upon executing the command, a directory named ''SeqSero_result_Time_your_run'' + will be created. Your result will be stored in ''SeqSero_result.txt'' in that + directory. And the assembled alleles can also be found in the directory if using + "-m a" (allele mode)' + bio.tool id: seqsero2 + bio.tool ids: + - seqsero2 + bio.tool name: SeqSero2 +- Available on UseGalaxy.eu: 15 + Available on UseGalaxy.fr: 15 + Available on UseGalaxy.org (Main): 15 + Available on UseGalaxy.org.au: 15 + Conda id: seqtk + Conda version: '1.4' + Date of first commit of the suite: '2017-01-20' + Description: Toolkit for processing sequences in FASTA/Q formats + EDAM operation: + - Data handling + - Sequence file editing + EDAM operation (no superclasses): + - Data handling + - Sequence file editing + EDAM topic: + - Data management + EDAM topic (no superclasses): [] + Galaxy tool ids: + - seqtk_comp + - seqtk_cutN + - seqtk_dropse + - seqtk_fqchk + - seqtk_hety + - seqtk_listhet + - seqtk_mergefa + - seqtk_mergepe + - seqtk_mutfa + - seqtk_randbase + - seqtk_sample + - seqtk_seq + - seqtk_subseq + - seqtk_telo + - seqtk_trimfq + Galaxy wrapper id: seqtk + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk + Galaxy wrapper version: '1.4' + No. of tool users (5 years) (usegalaxy.eu): 72816 + No. of tool users (5 years) (usegalaxy.org): 102777 + No. of tool users (5 years) (usegalaxy.org.au): 154613 + No. of tool users (5 years) - all main servers: 330206 + No. of tool users (all time) (usegalaxy.eu): 73514 + No. of tool users (all time) (usegalaxy.org): 107831 + No. of tool users (all time) (usegalaxy.org.au): 154613 + No. of tool users (all time) - all main servers: 335958 + Source: https://github.com/lh3/seqtk + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2210 + Tool usage (5 years) (usegalaxy.org): 2313 + Tool usage (5 years) (usegalaxy.org.au): 682 + Tool usage (5 years) - all main servers: 5205 + Tool usage (all time) (usegalaxy.eu): 2300 + Tool usage (all time) (usegalaxy.org): 2669 + Tool usage (all time) (usegalaxy.org.au): 682 + Tool usage (all time) - all main servers: 5651 + ToolShed categories: + - Sequence Analysis + ToolShed id: seqtk + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 14 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 14 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 14 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 15 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 14 + Tools available on UseGalaxy.cz: 14 + Tools available on UseGalaxy.eu: 15 + Tools available on UseGalaxy.fr: 15 + Tools available on UseGalaxy.no: 14 + Tools available on UseGalaxy.org (Main): 15 + Tools available on UseGalaxy.org.au: 15 + Tools available on Viral Variant Visualizer (VVV): 14 + availability: + UseGalaxy.be: 14 + UseGalaxy.cz: 14 + UseGalaxy.eu: 15 + UseGalaxy.fr: 15 + UseGalaxy.no: 14 + UseGalaxy.or: 15 + biii: null + bio.tool description: A tool for processing sequences in the FASTA or FASTQ format. + It parses both FASTA and FASTQ files which can also be optionally compressed by + gzip. + bio.tool id: seqtk + bio.tool ids: + - seqtk + bio.tool name: seqtk +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: seqwish + Conda version: 0.7.11 + Date of first commit of the suite: '2020-04-06' + Description: Alignment to variation graph inducer + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - seqwish + Galaxy wrapper id: seqwish + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ + Galaxy wrapper version: 0.7.5 + No. of tool users (5 years) (usegalaxy.eu): 271 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 271 + No. of tool users (all time) (usegalaxy.eu): 271 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 271 + Source: https://github.com/ekg/seqwish + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Sequence Analysis + - Variant Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-seurat + Conda version: 3.0.2 + Date of first commit of the suite: '2020-07-22' + Description: Seurat - R toolkit for single cell genomics + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - seurat_create + - seurat_data + - seurat_integrate + - seurat_clustering + - seurat_preprocessing + - seurat_plot + - seurat_reduce_dimension + Galaxy wrapper id: seurat + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 + Galaxy wrapper version: '5.0' + No. of tool users (5 years) (usegalaxy.eu): 121 + No. of tool users (5 years) (usegalaxy.org): 32 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 153 + No. of tool users (all time) (usegalaxy.eu): 121 + No. of tool users (all time) (usegalaxy.org): 32 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 153 + Source: https://satijalab.org/seurat/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 5 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 16 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 5 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 16 + ToolShed categories: + - Single Cell + - Transcriptomics + - Sequence Analysis + ToolShed id: seurat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 7 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 7 + UseGalaxy.fr: 7 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: shasta + Conda version: 0.13.0 + Date of first commit of the suite: '2020-11-11' + Description: Fast de novo assembly of long read sequencing data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - shasta + Galaxy wrapper id: shasta + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta + Galaxy wrapper version: 0.6.0 + No. of tool users (5 years) (usegalaxy.eu): 913 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 568 + No. of tool users (5 years) - all main servers: 1481 + No. of tool users (all time) (usegalaxy.eu): 913 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 568 + No. of tool users (all time) - all main servers: 1481 + Source: https://github.com/chanzuckerberg/shasta + Status: To update + Tool usage (5 years) (usegalaxy.eu): 308 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 73 + Tool usage (5 years) - all main servers: 381 + Tool usage (all time) (usegalaxy.eu): 308 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 73 + Tool usage (all time) - all main servers: 381 + ToolShed categories: + - Assembly + - Nanopore + ToolShed id: shasta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: shorah + Conda version: 1.99.2 + Date of first commit of the suite: '2018-11-27' + Description: Reconstruct haplotypes using ShoRAH in amplicon mode + EDAM operation: + - Haplotype mapping + - Variant calling + EDAM operation (no superclasses): + - Haplotype mapping + - Variant calling + EDAM topic: + - Metagenomics + - Sequencing + - Genetics + EDAM topic (no superclasses): + - Metagenomics + - Sequencing + - Genetics + Galaxy tool ids: + - shorah_amplicon + Galaxy wrapper id: shorah + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah + Galaxy wrapper version: 1.1.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/cbg-ethz/shorah/blob/master/README.md + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: shorah_amplicon + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: Inference of a population from a set of short reads. The package + contains programs that support mapping of reads to a reference genome, correcting + sequencing errors by locally clustering reads in small windows of the alignment, + reconstructing a minimal set of global haplotypes that explain the reads, and + estimating the frequencies of the inferred haplotypes. + bio.tool id: shorah + bio.tool ids: + - shorah + bio.tool name: ShoRAH +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: shovill + Conda version: 1.1.0 + Date of first commit of the suite: '2017-10-24' + Description: Faster de novo assembly pipeline based around Spades + EDAM operation: + - Genome assembly + EDAM operation (no superclasses): + - Genome assembly + EDAM topic: + - Genomics + - Microbiology + - Sequence assembly + EDAM topic (no superclasses): + - Genomics + - Microbiology + - Sequence assembly + Galaxy tool ids: + - shovill + Galaxy wrapper id: shovill + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 46125 + No. of tool users (5 years) (usegalaxy.org): 40577 + No. of tool users (5 years) (usegalaxy.org.au): 19960 + No. of tool users (5 years) - all main servers: 106662 + No. of tool users (all time) (usegalaxy.eu): 47376 + No. of tool users (all time) (usegalaxy.org): 40577 + No. of tool users (all time) (usegalaxy.org.au): 21130 + No. of tool users (all time) - all main servers: 109083 + Source: https://github.com/tseemann/shovill + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2273 + Tool usage (5 years) (usegalaxy.org): 3971 + Tool usage (5 years) (usegalaxy.org.au): 1085 + Tool usage (5 years) - all main servers: 7329 + Tool usage (all time) (usegalaxy.eu): 2356 + Tool usage (all time) (usegalaxy.org): 3971 + Tool usage (all time) (usegalaxy.org.au): 1199 + Tool usage (all time) - all main servers: 7526 + ToolShed categories: + - Assembly + ToolShed id: shovill + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Shovill is a pipeline for assembly of bacterial isolate genomes + from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the + steps before and after the primary assembly step to get similar results in less + time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so + you can take advantage of the pre- and post-processing the Shovill provides with + those too. + bio.tool id: shovill + bio.tool ids: + - shovill + bio.tool name: shovill +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: sickle-trim + Conda version: '1.33' + Date of first commit of the suite: '2015-11-03' + Description: A windowed adaptive trimming tool for FASTQ files using quality + EDAM operation: + - Sequence trimming + EDAM operation (no superclasses): + - Sequence trimming + EDAM topic: + - Data quality management + EDAM topic (no superclasses): + - Data quality management + Galaxy tool ids: + - sickle + Galaxy wrapper id: sickle + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle + Galaxy wrapper version: 1.33.2 + No. of tool users (5 years) (usegalaxy.eu): 18184 + No. of tool users (5 years) (usegalaxy.org): 10514 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 28698 + No. of tool users (all time) (usegalaxy.eu): 18937 + No. of tool users (all time) (usegalaxy.org): 10514 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 29451 + Source: https://github.com/najoshi/sickle + Status: To update + Tool usage (5 years) (usegalaxy.eu): 555 + Tool usage (5 years) (usegalaxy.org): 1063 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1618 + Tool usage (all time) (usegalaxy.eu): 608 + Tool usage (all time) (usegalaxy.org): 1063 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1671 + ToolShed categories: + - Fastq Manipulation + - Sequence Analysis + ToolShed id: sickle + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool that uses sliding windows along with quality and length + thresholds to determine when quality is sufficiently low to trim the 3'-end of + reads and also determines when the quality is sufficiently high enough to trim + the 5'-end of reads. + bio.tool id: sickle + bio.tool ids: + - sickle + bio.tool name: sickle +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 2 + Conda id: r-argparse + Conda version: 1.0.1 + Date of first commit of the suite: '2021-02-28' + Description: A text mining framework for interactive analysis and visualization + of similarities among biomedical entities. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - abstracts_by_pmids + - pmids_to_pubtator_matrix + - pubmed_by_queries + - text_to_wordmatrix + Galaxy wrapper id: simtext + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tools/simtext + Galaxy wrapper version: 0.0.2 + No. of tool users (5 years) (usegalaxy.eu): 220 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 416 + No. of tool users (5 years) - all main servers: 636 + No. of tool users (all time) (usegalaxy.eu): 220 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 416 + No. of tool users (all time) - all main servers: 636 + Source: https://github.com/dlal-group/simtext + Status: To update + Tool usage (5 years) (usegalaxy.eu): 68 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 10 + Tool usage (5 years) - all main servers: 78 + Tool usage (all time) (usegalaxy.eu): 68 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 10 + Tool usage (all time) - all main servers: 78 + ToolShed categories: + - Text Manipulation + ToolShed id: simtext + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: sina + Conda version: 1.7.2 + Date of first commit of the suite: '2019-10-11' + Description: SINA reference based multiple sequence alignment + EDAM operation: + - Sequence alignment analysis + - Multiple sequence alignment + - Taxonomic classification + - Structure-based sequence alignment + EDAM operation (no superclasses): + - Sequence alignment analysis + - Multiple sequence alignment + - Taxonomic classification + - Structure-based sequence alignment + EDAM topic: + - Sequencing + - RNA + - Nucleic acid structure analysis + - Taxonomy + - Sequence analysis + - Taxonomy + EDAM topic (no superclasses): + - Sequencing + - RNA + - Nucleic acid structure analysis + - Taxonomy + - Sequence analysis + - Taxonomy + Galaxy tool ids: + - sina + Galaxy wrapper id: sina + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina + Galaxy wrapper version: 1.7.2 + No. of tool users (5 years) (usegalaxy.eu): 1369 + No. of tool users (5 years) (usegalaxy.org): 2398 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3767 + No. of tool users (all time) (usegalaxy.eu): 1369 + No. of tool users (all time) (usegalaxy.org): 2398 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3767 + Source: https://sina.readthedocs.io/en/latest/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 125 + Tool usage (5 years) (usegalaxy.org): 420 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 545 + Tool usage (all time) (usegalaxy.eu): 125 + Tool usage (all time) (usegalaxy.org): 420 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 545 + ToolShed categories: + - Sequence Analysis + ToolShed id: sina + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Aligns and optionally taxonomically classifies your rRNA gene + sequences.Reference based multiple sequence alignment + bio.tool id: sina + bio.tool ids: + - sina + bio.tool name: SINA +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: sinto + Conda version: 0.10.1 + Date of first commit of the suite: '2023-04-12' + Description: Sinto single-cell analysis tools + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sinto_barcode + - sinto_fragments + Galaxy wrapper id: sinto + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto + Galaxy wrapper version: 0.10.1 + No. of tool users (5 years) (usegalaxy.eu): 284 + No. of tool users (5 years) (usegalaxy.org): 165 + No. of tool users (5 years) (usegalaxy.org.au): 14 + No. of tool users (5 years) - all main servers: 463 + No. of tool users (all time) (usegalaxy.eu): 284 + No. of tool users (all time) (usegalaxy.org): 165 + No. of tool users (all time) (usegalaxy.org.au): 14 + No. of tool users (all time) - all main servers: 463 + Source: https://github.com/timoast/sinto + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 70 + Tool usage (5 years) (usegalaxy.org): 38 + Tool usage (5 years) (usegalaxy.org.au): 2 + Tool usage (5 years) - all main servers: 110 + Tool usage (all time) (usegalaxy.eu): 70 + Tool usage (all time) (usegalaxy.org): 38 + Tool usage (all time) (usegalaxy.org.au): 2 + Tool usage (all time) - all main servers: 110 + ToolShed categories: + - Single Cell + - Epigenetics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: slamdunk + Conda version: 0.4.3 + Date of first commit of the suite: '2019-01-20' + Description: Slamdunk maps and quantifies SLAMseq reads + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - alleyoop + - slamdunk + Galaxy wrapper id: slamdunk + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk + Galaxy wrapper version: 0.4.3 + No. of tool users (5 years) (usegalaxy.eu): 346 + No. of tool users (5 years) (usegalaxy.org): 872 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1218 + No. of tool users (all time) (usegalaxy.eu): 362 + No. of tool users (all time) (usegalaxy.org): 872 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1234 + Source: http://t-neumann.github.io/slamdunk + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 67 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 83 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 67 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 83 + ToolShed categories: + - RNA + - Transcriptomics + - Sequence Analysis + - Next Gen Mappers + ToolShed id: slamdunk + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-sleuth + Conda version: 0.30.1 + Date of first commit of the suite: '2023-05-31' + Description: Sleuth is a program for differential analysis of RNA-Seq data. + EDAM operation: + - Expression data visualisation + - Differential gene expression analysis + - Gene expression profiling + - Statistical calculation + EDAM operation (no superclasses): + - Expression data visualisation + - Differential gene expression analysis + - Gene expression profiling + - Statistical calculation + EDAM topic: + - RNA-seq + - Gene expression + - Statistics and probability + EDAM topic (no superclasses): + - Gene expression + - Statistics and probability + Galaxy tool ids: + - sleuth + Galaxy wrapper id: sleuth + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth + Galaxy wrapper version: 0.30.1 + No. of tool users (5 years) (usegalaxy.eu): 141 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 141 + No. of tool users (all time) (usegalaxy.eu): 141 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 141 + Source: https://github.com/pachterlab/sleuth + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 26 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 26 + Tool usage (all time) (usegalaxy.eu): 26 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 26 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + ToolShed id: sleuth + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: A statistical model and software application for RNA-seq differential + expression analysis. + bio.tool id: sleuth + bio.tool ids: + - sleuth + bio.tool name: sleuth +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: smallgenomeutilities + Conda version: 0.4.1 + Date of first commit of the suite: '2023-05-30' + Description: Set of utilities for manipulating small viral genome data. + EDAM operation: + - Read pre-processing + - Sequence alignment + - Genetic variation analysis + EDAM operation (no superclasses): + - Read pre-processing + - Sequence alignment + - Genetic variation analysis + EDAM topic: + - Genomics + - Population genetics + - Workflows + - Virology + - Sequencing + EDAM topic (no superclasses): + - Genomics + - Population genetics + - Workflows + - Virology + - Sequencing + Galaxy tool ids: + - smgu_frameshift_deletions_checks + Galaxy wrapper id: smallgenomeutilities + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities + Galaxy wrapper version: 0.4.1 + No. of tool users (5 years) (usegalaxy.eu): 158 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 158 + No. of tool users (all time) (usegalaxy.eu): 158 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 158 + Source: https://github.com/cbg-ethz/smallgenomeutilities + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Sequence Analysis + ToolShed id: smallgenomeutilities + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Bioinformatics pipeline for the analysis of next-generation + sequencing data derived from intra-host viral populations. + bio.tool id: v-pipe + bio.tool ids: + - v-pipe + bio.tool name: V-pipe +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: smudgeplot + Conda version: 0.3.0 + Date of first commit of the suite: '2022-06-30' + Description: Inference of ploidy and heterozygosity structure using whole genome + sequencing + EDAM operation: + - Sequence trimming + - Genotyping + - k-mer counting + EDAM operation (no superclasses): + - Sequence trimming + - Genotyping + - k-mer counting + EDAM topic: + - Sequence assembly + - Genetic variation + - Mathematics + EDAM topic (no superclasses): + - Sequence assembly + - Genetic variation + - Mathematics + Galaxy tool ids: + - smudgeplot + Galaxy wrapper id: smudgeplot + Galaxy wrapper owner: galaxy-australia + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc + Galaxy wrapper version: 0.2.5 + No. of tool users (5 years) (usegalaxy.eu): 325 + No. of tool users (5 years) (usegalaxy.org): 137 + No. of tool users (5 years) (usegalaxy.org.au): 843 + No. of tool users (5 years) - all main servers: 1305 + No. of tool users (all time) (usegalaxy.eu): 325 + No. of tool users (all time) (usegalaxy.org): 137 + No. of tool users (all time) (usegalaxy.org.au): 843 + No. of tool users (all time) - all main servers: 1305 + Source: https://github.com/KamilSJaron/smudgeplot + Status: To update + Tool usage (5 years) (usegalaxy.eu): 61 + Tool usage (5 years) (usegalaxy.org): 54 + Tool usage (5 years) (usegalaxy.org.au): 63 + Tool usage (5 years) - all main servers: 178 + Tool usage (all time) (usegalaxy.eu): 61 + Tool usage (all time) (usegalaxy.org): 54 + Tool usage (all time) (usegalaxy.org.au): 63 + Tool usage (all time) - all main servers: 178 + ToolShed categories: + - Assembly + ToolShed id: smudgeplot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: 'Reference-free profiling of polyploid genomes | Inference + of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots + are computed from raw or even better from trimmed reads and show the haplotype + structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous + kmer pairs from kmer dump files and performs gymnastics with them. We are able + to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also + allows us to analyze obscure genomes with duplications, various ploidy levels, + etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes + Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; + doi: https://doi.org/10.1101/747568' + bio.tool id: smudgeplots + bio.tool ids: + - smudgeplots + bio.tool name: Smudgeplots +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: snap + Conda version: '2013_11_29' + Date of first commit of the suite: '2017-10-12' + Description: SNAP is a general purpose gene finding program suitable for both eukaryotic + and prokaryotic genomes. + EDAM operation: + - Gene prediction + EDAM operation (no superclasses): + - Gene prediction + EDAM topic: + - DNA + - DNA polymorphism + - Genetics + EDAM topic (no superclasses): + - DNA polymorphism + - Genetics + Galaxy tool ids: + - snap + - snap_training + Galaxy wrapper id: snap + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap + Galaxy wrapper version: '2013_11_29' + No. of tool users (5 years) (usegalaxy.eu): 1499 + No. of tool users (5 years) (usegalaxy.org): 779 + No. of tool users (5 years) (usegalaxy.org.au): 467 + No. of tool users (5 years) - all main servers: 2745 + No. of tool users (all time) (usegalaxy.eu): 1638 + No. of tool users (all time) (usegalaxy.org): 779 + No. of tool users (all time) (usegalaxy.org.au): 467 + No. of tool users (all time) - all main servers: 2884 + Source: https://github.com/KorfLab/SNAP + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 331 + Tool usage (5 years) (usegalaxy.org): 244 + Tool usage (5 years) (usegalaxy.org.au): 83 + Tool usage (5 years) - all main servers: 658 + Tool usage (all time) (usegalaxy.eu): 358 + Tool usage (all time) (usegalaxy.org): 244 + Tool usage (all time) (usegalaxy.org.au): 83 + Tool usage (all time) - all main servers: 685 + ToolShed categories: + - Sequence Analysis + ToolShed id: snap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: The Semi-HMM-based Nucleic Acid Parser is a gene prediction + tool. + bio.tool id: snap + bio.tool ids: + - snap + bio.tool name: SNAP +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 4 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-05-16' + Description: "SnapATAC2 \u2013 A Python/Rust package for single-cell epigenomics\ + \ analysis" + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - snapatac2_clustering + - snapatac2_peaks_and_motif + - snapatac2_plotting + - snapatac2_preprocessing + Galaxy wrapper id: snapatac2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 + Galaxy wrapper version: 2.6.4 + No. of tool users (5 years) (usegalaxy.eu): 1817 + No. of tool users (5 years) (usegalaxy.org): 4 + No. of tool users (5 years) (usegalaxy.org.au): 136 + No. of tool users (5 years) - all main servers: 1957 + No. of tool users (all time) (usegalaxy.eu): 1817 + No. of tool users (all time) (usegalaxy.org): 4 + No. of tool users (all time) (usegalaxy.org.au): 136 + No. of tool users (all time) - all main servers: 1957 + Source: https://kzhang.org/SnapATAC2/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 14 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 20 + Tool usage (all time) (usegalaxy.eu): 14 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 20 + ToolShed categories: + - Single Cell + - Epigenetics + ToolShed id: snapatac2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 4 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 4 + UseGalaxy.or: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: sniffles + Conda version: '2.4' + Date of first commit of the suite: '2020-08-29' + Description: Galaxy wrapper for sniffles + EDAM operation: + - Sequence analysis + - Structural variation detection + EDAM operation (no superclasses): + - Sequence analysis + - Structural variation detection + EDAM topic: + - DNA structural variation + - Sequencing + EDAM topic (no superclasses): + - Sequencing + Galaxy tool ids: + - sniffles + Galaxy wrapper id: sniffles + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc + Galaxy wrapper version: '2.4' + No. of tool users (5 years) (usegalaxy.eu): 1141 + No. of tool users (5 years) (usegalaxy.org): 606 + No. of tool users (5 years) (usegalaxy.org.au): 2267 + No. of tool users (5 years) - all main servers: 4014 + No. of tool users (all time) (usegalaxy.eu): 1141 + No. of tool users (all time) (usegalaxy.org): 606 + No. of tool users (all time) (usegalaxy.org.au): 2267 + No. of tool users (all time) - all main servers: 4014 + Source: https://github.com/fritzsedlazeck/Sniffles + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 134 + Tool usage (5 years) (usegalaxy.org): 156 + Tool usage (5 years) (usegalaxy.org.au): 80 + Tool usage (5 years) - all main servers: 370 + Tool usage (all time) (usegalaxy.eu): 134 + Tool usage (all time) (usegalaxy.org): 156 + Tool usage (all time) (usegalaxy.org.au): 80 + Tool usage (all time) - all main servers: 370 + ToolShed categories: + - Sequence Analysis + ToolShed id: sniffles + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: An algorithm for structural variation detection from third + generation sequencing alignment. + bio.tool id: sniffles + bio.tool ids: + - sniffles + bio.tool name: Sniffles +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: snipit + Conda version: '1.2' + Date of first commit of the suite: '2022-07-17' + Description: Summarise snps relative to a reference sequence + EDAM operation: + - Base position variability plotting + EDAM operation (no superclasses): + - Base position variability plotting + EDAM topic: + - Virology + EDAM topic (no superclasses): + - Virology + Galaxy tool ids: + - snipit + Galaxy wrapper id: snipit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit + Galaxy wrapper version: '1.2' + No. of tool users (5 years) (usegalaxy.eu): 905 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 905 + No. of tool users (all time) (usegalaxy.eu): 905 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 905 + Source: https://github.com/aineniamh/snipit + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 44 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 44 + Tool usage (all time) (usegalaxy.eu): 44 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 44 + ToolShed categories: + - Variant Analysis + - Sequence Analysis + ToolShed id: snipit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Summarise snps relative to a reference sequence + bio.tool id: snipit + bio.tool ids: + - snipit + bio.tool name: snipit +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: snippy + Conda version: 4.6.0 + Date of first commit of the suite: '2019-04-02' + Description: Contains the snippy tool for characterising microbial snps + EDAM operation: + - Phylogenetic tree visualisation + - Phylogenetic tree generation + - Variant calling + EDAM operation (no superclasses): + - Phylogenetic tree visualisation + - Variant calling + EDAM topic: + - Genomics + - Model organisms + - DNA polymorphism + - Phylogenetics + EDAM topic (no superclasses): + - Genomics + - Model organisms + - DNA polymorphism + - Phylogenetics + Galaxy tool ids: + - snippy_core + - snippy + - snippy_clean_full_aln + Galaxy wrapper id: snippy + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 121363 + No. of tool users (5 years) (usegalaxy.org): 92504 + No. of tool users (5 years) (usegalaxy.org.au): 48068 + No. of tool users (5 years) - all main servers: 261935 + No. of tool users (all time) (usegalaxy.eu): 124773 + No. of tool users (all time) (usegalaxy.org): 92504 + No. of tool users (all time) (usegalaxy.org.au): 52034 + No. of tool users (all time) - all main servers: 269311 + Source: https://github.com/tseemann/snippy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3448 + Tool usage (5 years) (usegalaxy.org): 3945 + Tool usage (5 years) (usegalaxy.org.au): 2705 + Tool usage (5 years) - all main servers: 10098 + Tool usage (all time) (usegalaxy.eu): 3602 + Tool usage (all time) (usegalaxy.org): 3945 + Tool usage (all time) (usegalaxy.org.au): 3073 + Tool usage (all time) - all main servers: 10620 + ToolShed categories: + - Sequence Analysis + ToolShed id: snippy + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + UseGalaxy.no: 2 + UseGalaxy.or: 3 + biii: null + bio.tool description: Rapid haploid variant calling and core SNP phylogeny generation. + bio.tool id: snippy + bio.tool ids: + - snippy + bio.tool name: snippy +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: snp-dists + Conda version: 0.8.2 + Date of first commit of the suite: '2019-10-18' + Description: Compute pairwise SNP distance matrix from a FASTA sequence alignment + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - snp_dists + Galaxy wrapper id: snp-dists + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists + Galaxy wrapper version: 0.8.2 + No. of tool users (5 years) (usegalaxy.eu): 6555 + No. of tool users (5 years) (usegalaxy.org): 5336 + No. of tool users (5 years) (usegalaxy.org.au): 1143 + No. of tool users (5 years) - all main servers: 13034 + No. of tool users (all time) (usegalaxy.eu): 6555 + No. of tool users (all time) (usegalaxy.org): 5336 + No. of tool users (all time) (usegalaxy.org.au): 1143 + No. of tool users (all time) - all main servers: 13034 + Source: https://github.com/tseemann/snp-dists + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 807 + Tool usage (5 years) (usegalaxy.org): 171 + Tool usage (5 years) (usegalaxy.org.au): 182 + Tool usage (5 years) - all main servers: 1160 + Tool usage (all time) (usegalaxy.eu): 807 + Tool usage (all time) (usegalaxy.org): 171 + Tool usage (all time) (usegalaxy.org.au): 182 + Tool usage (all time) - all main servers: 1160 + ToolShed categories: + - Variant Analysis + ToolShed id: snp_dists + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: snp-sites + Conda version: 2.5.1 + Date of first commit of the suite: '2017-06-28' + Description: Finds SNP sites from a multi-FASTA alignment file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - snp_sites + Galaxy wrapper id: snp-sites + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites + Galaxy wrapper version: 2.5.1 + No. of tool users (5 years) (usegalaxy.eu): 6597 + No. of tool users (5 years) (usegalaxy.org): 1467 + No. of tool users (5 years) (usegalaxy.org.au): 1279 + No. of tool users (5 years) - all main servers: 9343 + No. of tool users (all time) (usegalaxy.eu): 6597 + No. of tool users (all time) (usegalaxy.org): 1467 + No. of tool users (all time) (usegalaxy.org.au): 1279 + No. of tool users (all time) - all main servers: 9343 + Source: https://github.com/sanger-pathogens/snp-sites + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 663 + Tool usage (5 years) (usegalaxy.org): 256 + Tool usage (5 years) (usegalaxy.org.au): 114 + Tool usage (5 years) - all main servers: 1033 + Tool usage (all time) (usegalaxy.eu): 663 + Tool usage (all time) (usegalaxy.org): 256 + Tool usage (all time) (usegalaxy.org.au): 114 + Tool usage (all time) - all main servers: 1033 + ToolShed categories: + - Variant Analysis + ToolShed id: snp_sites + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-06-17' + Description: SnpEff, the COVID-19 version, is a genetic variant annotation and effect + prediction toolbox + EDAM operation: + - SNP detection + EDAM operation (no superclasses): + - SNP detection + EDAM topic: + - DNA polymorphism + - Genetic variation + - Nucleic acid sites, features and motifs + EDAM topic (no superclasses): + - DNA polymorphism + - Nucleic acid sites, features and motifs + Galaxy tool ids: + - snpeff_sars_cov_2 + Galaxy wrapper id: snpeff-covid19 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 764895 + No. of tool users (5 years) (usegalaxy.org): 94572 + No. of tool users (5 years) (usegalaxy.org.au): 26990 + No. of tool users (5 years) - all main servers: 886457 + No. of tool users (all time) (usegalaxy.eu): 764895 + No. of tool users (all time) (usegalaxy.org): 94572 + No. of tool users (all time) (usegalaxy.org.au): 26990 + No. of tool users (all time) - all main servers: 886457 + Source: http://snpeff.sourceforge.net/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1276 + Tool usage (5 years) (usegalaxy.org): 1636 + Tool usage (5 years) (usegalaxy.org.au): 561 + Tool usage (5 years) - all main servers: 3473 + Tool usage (all time) (usegalaxy.eu): 1276 + Tool usage (all time) (usegalaxy.org): 1636 + Tool usage (all time) (usegalaxy.org.au): 561 + Tool usage (all time) - all main servers: 3473 + ToolShed categories: + - Genome-Wide Association Study + - Variant Analysis + ToolShed id: snpeff_sars_cov_2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Variant annotation and effect prediction tool. It annotates + and predicts the effects of variants on genes and proteins (such as amino acid + changes). + bio.tool id: snpeff + bio.tool ids: + - snpeff + bio.tool name: snpEff +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2020-12-02' + Description: A plotting app to visualise the SNPs across a region + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - snpfreqplot + Galaxy wrapper id: snpfreqplot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 3683 + No. of tool users (5 years) (usegalaxy.org): 1401 + No. of tool users (5 years) (usegalaxy.org.au): 1029 + No. of tool users (5 years) - all main servers: 6113 + No. of tool users (all time) (usegalaxy.eu): 3683 + No. of tool users (all time) (usegalaxy.org): 1401 + No. of tool users (all time) (usegalaxy.org.au): 1029 + No. of tool users (all time) - all main servers: 6113 + Source: https://github.com/BrownfieldPlantLab/SNPFreqPlot + Status: To update + Tool usage (5 years) (usegalaxy.eu): 338 + Tool usage (5 years) (usegalaxy.org): 433 + Tool usage (5 years) (usegalaxy.org.au): 95 + Tool usage (5 years) - all main servers: 866 + Tool usage (all time) (usegalaxy.eu): 338 + Tool usage (all time) (usegalaxy.org): 433 + Tool usage (all time) (usegalaxy.org.au): 95 + Tool usage (all time) - all main servers: 866 + ToolShed categories: + - Variant Analysis + ToolShed id: snpfreqplot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: socru + Conda version: 2.2.4 + Date of first commit of the suite: '2019-09-03' + Description: Order and orientation of complete bacterial genomes + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - socru + Galaxy wrapper id: socru + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru + Galaxy wrapper version: 2.1.7 + No. of tool users (5 years) (usegalaxy.eu): 659 + No. of tool users (5 years) (usegalaxy.org): 296 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 955 + No. of tool users (all time) (usegalaxy.eu): 659 + No. of tool users (all time) (usegalaxy.org): 296 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 955 + Source: https://github.com/quadram-institute-bioscience/socru + Status: To update + Tool usage (5 years) (usegalaxy.eu): 42 + Tool usage (5 years) (usegalaxy.org): 92 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 134 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 92 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 134 + ToolShed categories: + - Sequence Analysis + ToolShed id: socru + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: sonneityping + Conda version: '20210201' + Date of first commit of the suite: '2021-09-16' + Description: Scripts for parsing Mykrobe predict results for Shigella sonnei. + EDAM operation: + - Antimicrobial resistance prediction + - Variant calling + - Genotyping + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + - Variant calling + - Genotyping + EDAM topic: + - Whole genome sequencing + - Genotype and phenotype + - Genetic variation + - Metagenomics + EDAM topic (no superclasses): + - Whole genome sequencing + - Genotype and phenotype + - Genetic variation + - Metagenomics + Galaxy tool ids: + - sonneityping + Galaxy wrapper id: sonneityping + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping + Galaxy wrapper source: https://github.com/katholt/sonneityping + Galaxy wrapper version: '20210201' + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1 + Source: https://github.com/katholt/sonneityping + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Sequence Analysis + ToolShed id: sonneityping + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Scripts for parsing Mykrobe predict results for Shigella sonnei. + bio.tool id: sonneityping + bio.tool ids: + - sonneityping + bio.tool name: sonneityping +- Available on UseGalaxy.eu: 9 + Available on UseGalaxy.fr: 9 + Available on UseGalaxy.org (Main): 9 + Available on UseGalaxy.org.au: 9 + Conda id: spades + Conda version: 4.0.0 + Date of first commit of the suite: '2017-06-30' + Description: 'SPAdes is an assembly toolkit containing various assembly pipelines. + It implements the following 4 stages: assembly graph construction, k-bimer adjustment, + construction of paired assembly graph and contig construction.' + EDAM operation: + - Genome assembly + EDAM operation (no superclasses): + - Genome assembly + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - spades_biosyntheticspades + - spades_coronaspades + - spades_metaplasmidspades + - metaspades + - spades_metaviralspades + - spades_plasmidspades + - rnaspades + - spades_rnaviralspades + - spades + Galaxy wrapper id: spades + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades + Galaxy wrapper version: 3.15.5 + No. of tool users (5 years) (usegalaxy.eu): 82716 + No. of tool users (5 years) (usegalaxy.org): 120471 + No. of tool users (5 years) (usegalaxy.org.au): 54067 + No. of tool users (5 years) - all main servers: 257254 + No. of tool users (all time) (usegalaxy.eu): 87113 + No. of tool users (all time) (usegalaxy.org): 120475 + No. of tool users (all time) (usegalaxy.org.au): 61541 + No. of tool users (all time) - all main servers: 269129 + Source: https://github.com/ablab/spades + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8209 + Tool usage (5 years) (usegalaxy.org): 14787 + Tool usage (5 years) (usegalaxy.org.au): 5817 + Tool usage (5 years) - all main servers: 28813 + Tool usage (all time) (usegalaxy.eu): 8526 + Tool usage (all time) (usegalaxy.org): 14790 + Tool usage (all time) (usegalaxy.org.au): 6653 + Tool usage (all time) - all main servers: 29969 + ToolShed categories: + - Assembly + - RNA + - Metagenomics + ToolShed id: spades + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 3 + Tools available on GalaxyTrakr: 8 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 3 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 9 + Tools available on UseGalaxy.eu: 9 + Tools available on UseGalaxy.fr: 9 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 9 + Tools available on UseGalaxy.org.au: 9 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 9 + UseGalaxy.eu: 9 + UseGalaxy.fr: 3 + UseGalaxy.no: 3 + UseGalaxy.or: 9 + biii: null + bio.tool description: "St. Petersburg genome assembler \u2013 is intended for both\ + \ standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works\ + \ with Illumina or IonTorrent reads and is capable of providing hybrid assemblies\ + \ using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided\ + \ and can be used as long reads." + bio.tool id: spades + bio.tool ids: + - plasmidspades + - metaplasmidspades + - rnaspades + - metaspades + - spades + - coronaspades + - metaviralspades + - biosyntheticspades + - rnaviralspades + bio.tool name: SPAdes +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-01-11' + Description: Spaln (space-efficient spliced alignment) maps and aligns a set of + cDNA or protein sequences onto a whole genomic sequence. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - list_spaln_tables + - spaln + Galaxy wrapper id: spaln + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln + Galaxy wrapper source: https://github.com/ogotoh/spaln + Galaxy wrapper version: 2.4.9 + No. of tool users (5 years) (usegalaxy.eu): 450 + No. of tool users (5 years) (usegalaxy.org): 4270 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4720 + No. of tool users (all time) (usegalaxy.eu): 491 + No. of tool users (all time) (usegalaxy.org): 4270 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4761 + Source: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 91 + Tool usage (5 years) (usegalaxy.org): 288 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 379 + Tool usage (all time) (usegalaxy.eu): 100 + Tool usage (all time) (usegalaxy.org): 288 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 388 + ToolShed categories: + - Sequence Analysis + - Genome annotation + ToolShed id: spaln + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: spapros + Conda version: 0.1.5 + Date of first commit of the suite: '2024-08-25' + Description: Select and evaluate probe sets for targeted spatial transcriptomics. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - spapros_evaluation + - spapros_selection + Galaxy wrapper id: spapros + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ + Galaxy wrapper version: 0.1.5 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/theislab/spapros + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Single Cell + - Transcriptomics + - Sequence Analysis + ToolShed id: spapros + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: spotyping + Conda version: '2.1' + Date of first commit of the suite: '2018-05-07' + Description: SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping + from sequence reads + EDAM operation: + - Variant pattern analysis + EDAM operation (no superclasses): + - Variant pattern analysis + EDAM topic: + - Microbiology + - Sequencing + - Sequence composition, complexity and repeats + - Genetic variation + EDAM topic (no superclasses): + - Microbiology + - Sequencing + - Sequence composition, complexity and repeats + - Genetic variation + Galaxy tool ids: + - spotyping + Galaxy wrapper id: spotyping + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping + Galaxy wrapper source: https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine + Galaxy wrapper version: '2.1' + No. of tool users (5 years) (usegalaxy.eu): 1436 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1436 + No. of tool users (all time) (usegalaxy.eu): 1436 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1436 + Source: https://github.com/xiaeryu/SpoTyping-v2.0 + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 23 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 23 + Tool usage (all time) (usegalaxy.eu): 23 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 23 + ToolShed categories: + - Sequence Analysis + ToolShed id: spotyping + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Fast and accurate in silico Mycobacterium spoligotyping from + sequence reads. + bio.tool id: spotyping + bio.tool ids: + - spotyping + bio.tool name: SpoTyping +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: spyboat + Conda version: null + Date of first commit of the suite: '2020-11-28' + Description: Wavelet analysis for 3d-image stacks + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - spyboat + Galaxy wrapper id: spyboat + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 142 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 142 + No. of tool users (all time) (usegalaxy.eu): 142 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 142 + Source: http://github.com/tensionhead/spyboat + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Imaging + - Graphics + ToolShed id: spyboat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: sra-tools + Conda version: 3.1.1 + Date of first commit of the suite: '2020-06-23' + Description: NCBI Sequence Read Archive toolkit utilities + EDAM operation: + - Data handling + EDAM operation (no superclasses): + - Data handling + EDAM topic: + - DNA + - Genomics + - Sequencing + EDAM topic (no superclasses): + - DNA + - Genomics + - Sequencing + Galaxy tool ids: + - fasterq_dump + - fastq_dump + - sam_dump + Galaxy wrapper id: sra-tools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools + Galaxy wrapper version: 3.1.1 + No. of tool users (5 years) (usegalaxy.eu): 364871 + No. of tool users (5 years) (usegalaxy.org): 583675 + No. of tool users (5 years) (usegalaxy.org.au): 48131 + No. of tool users (5 years) - all main servers: 996677 + No. of tool users (all time) (usegalaxy.eu): 376580 + No. of tool users (all time) (usegalaxy.org): 678448 + No. of tool users (all time) (usegalaxy.org.au): 50455 + No. of tool users (all time) - all main servers: 1105483 + Source: https://github.com/ncbi/sra-tools + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 16710 + Tool usage (5 years) (usegalaxy.org): 53271 + Tool usage (5 years) (usegalaxy.org.au): 5910 + Tool usage (5 years) - all main servers: 75891 + Tool usage (all time) (usegalaxy.eu): 17342 + Tool usage (all time) (usegalaxy.org): 59638 + Tool usage (all time) (usegalaxy.org.au): 6181 + Tool usage (all time) - all main servers: 83161 + ToolShed categories: + - Data Source + - Fastq Manipulation + ToolShed id: sra_tools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 3 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 3 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: The SRA Toolkit and SDK from NCBI is a collection of tools + and libraries for using data in the INSDC Sequence Read Archives. + bio.tool id: sra-tools + bio.tool ids: + - sra-tools + bio.tool name: SRA Software Toolkit +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: samtools + Conda version: '1.21' + Date of first commit of the suite: '2022-08-22' + Description: SRST2 Short Read Sequence Typing for Bacterial Pathogens + EDAM operation: + - Multilocus sequence typing + EDAM operation (no superclasses): + - Multilocus sequence typing + EDAM topic: + - Whole genome sequencing + - Public health and epidemiology + EDAM topic (no superclasses): + - Whole genome sequencing + - Public health and epidemiology + Galaxy tool ids: + - srst2 + Galaxy wrapper id: srst2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 + Galaxy wrapper source: https://github.com/katholt/srst2 + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 297 + No. of tool users (5 years) (usegalaxy.org): 71 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 368 + No. of tool users (all time) (usegalaxy.eu): 297 + No. of tool users (all time) (usegalaxy.org): 71 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 368 + Source: http://katholt.github.io/srst2/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 40 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 41 + Tool usage (all time) (usegalaxy.eu): 40 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 41 + ToolShed categories: + - Metagenomics + ToolShed id: srst2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: Short Read Sequence Typing for Bacterial Pathogens + bio.tool id: srst2 + bio.tool ids: + - srst2 + bio.tool name: srst2 +- Available on UseGalaxy.eu: 13 + Available on UseGalaxy.fr: 12 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 13 + Conda id: stacks + Conda version: '2.65' + Date of first commit of the suite: '2017-04-13' + Description: Stacks is a software pipeline for building loci from short-read sequences, + such as RAD-seq + EDAM operation: + - Data handling + EDAM operation (no superclasses): + - Data handling + EDAM topic: + - Mapping + - Population genetics + EDAM topic (no superclasses): + - Mapping + - Population genetics + Galaxy tool ids: + - stacks_assembleperead + - stacks_clonefilter + - stacks_cstacks + - stacks_denovomap + - stacks_genotypes + - stacks_populations + - stacks_procrad + - stacks_pstacks + - stacks_refmap + - stacks_rxstacks + - stacks_sstacks + - stacks_stats + - stacks_ustacks + Galaxy wrapper id: stacks + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 6440 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 4070 + No. of tool users (5 years) - all main servers: 10510 + No. of tool users (all time) (usegalaxy.eu): 11998 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 4070 + No. of tool users (all time) - all main servers: 16068 + Source: http://catchenlab.life.illinois.edu/stacks/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 465 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 76 + Tool usage (5 years) - all main servers: 541 + Tool usage (all time) (usegalaxy.eu): 593 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 76 + Tool usage (all time) - all main servers: 669 + ToolShed categories: + - Sequence Analysis + ToolShed id: stacks + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 11 + Tools available on UseGalaxy.cz: 13 + Tools available on UseGalaxy.eu: 13 + Tools available on UseGalaxy.fr: 12 + Tools available on UseGalaxy.no: 13 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 13 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 11 + UseGalaxy.cz: 13 + UseGalaxy.eu: 13 + UseGalaxy.fr: 12 + UseGalaxy.no: 13 + UseGalaxy.or: 13 + biii: null + bio.tool description: Developed to work with restriction enzyme based sequence data, + such as RADseq, for building genetic maps and conducting population genomics and + phylogeography analysis. + bio.tool id: stacks + bio.tool ids: + - stacks + bio.tool name: Stacks +- Available on UseGalaxy.eu: 12 + Available on UseGalaxy.fr: 12 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 12 + Conda id: stacks + Conda version: '2.65' + Date of first commit of the suite: '2019-09-30' + Description: Stacks is a software pipeline for building loci from short-read sequences, + such as RAD-seq + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - stacks2_clonefilter + - stacks2_cstacks + - stacks2_denovomap + - stacks2_gstacks + - stacks2_kmerfilter + - stacks2_populations + - stacks2_procrad + - stacks2_refmap + - stacks2_shortreads + - stacks2_sstacks + - stacks2_tsv2bam + - stacks2_ustacks + Galaxy wrapper id: stacks2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 + Galaxy wrapper version: '2.55' + No. of tool users (5 years) (usegalaxy.eu): 8437 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 18016 + No. of tool users (5 years) - all main servers: 26453 + No. of tool users (all time) (usegalaxy.eu): 8592 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 18016 + No. of tool users (all time) - all main servers: 26608 + Source: http://catchenlab.life.illinois.edu/stacks/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 626 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 270 + Tool usage (5 years) - all main servers: 896 + Tool usage (all time) (usegalaxy.eu): 646 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 270 + Tool usage (all time) - all main servers: 916 + ToolShed categories: + - Sequence Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 12 + Tools available on UseGalaxy.eu: 12 + Tools available on UseGalaxy.fr: 12 + Tools available on UseGalaxy.no: 12 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 12 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 12 + UseGalaxy.eu: 12 + UseGalaxy.fr: 12 + UseGalaxy.no: 12 + UseGalaxy.or: 12 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: star-fusion + Conda version: 1.13.0 + Date of first commit of the suite: '2015-10-15' + Description: STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - star_fusion + Galaxy wrapper id: star_fusion + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion + Galaxy wrapper version: 0.5.4-3+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 1312 + No. of tool users (5 years) (usegalaxy.org): 2198 + No. of tool users (5 years) (usegalaxy.org.au): 173 + No. of tool users (5 years) - all main servers: 3683 + No. of tool users (all time) (usegalaxy.eu): 1383 + No. of tool users (all time) (usegalaxy.org): 3076 + No. of tool users (all time) (usegalaxy.org.au): 173 + No. of tool users (all time) - all main servers: 4632 + Source: https://github.com/STAR-Fusion/STAR-Fusion + Status: To update + Tool usage (5 years) (usegalaxy.eu): 82 + Tool usage (5 years) (usegalaxy.org): 234 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 319 + Tool usage (all time) (usegalaxy.eu): 95 + Tool usage (all time) (usegalaxy.org): 303 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 401 + ToolShed categories: + - Sequence Analysis + - Transcriptomics + ToolShed id: star_fusion + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: straindesign + Conda version: 3.2.3 + Date of first commit of the suite: '2022-10-02' + Description: Toolbox to optimize biological model + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - straindesign_analyzing_model + - straindesign_reduce_model + - straindesign_simulate_deletion + Galaxy wrapper id: straindesign + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign + Galaxy wrapper source: https://github.com/brsynth/straindesign + Galaxy wrapper version: 3.2.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/brsynth/straindesign + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Systems Biology + - Synthetic Biology + ToolShed id: straindesign + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: strelka + Conda version: 2.9.10 + Date of first commit of the suite: '2021-01-27' + Description: Strelka2 is a fast and accurate small variant caller optimizedfor analysis + of germline variation in small cohorts and somaticvariation in tumor/normal sample + pairs. The germline caller employs anefficient tiered haplotype model to improve + accuracy and provide read-backedphasing, adaptively selecting between assembly + and a faster alignment-basedhaplotyping approach at each variant locus. The germline + caller also analyzesinput sequencing data using a mixture-model indel error estimation + method toimprove robustness to indel noise. The somatic calling model improves + on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor + possible tumor cell contamination in the normal sample. A final empiricalvariant + re-scoring step using random forest models trained on various callquality features + has been added to both callers to further improve precision. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - strelka_germline + - strelka_somatic + Galaxy wrapper id: strelka + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka + Galaxy wrapper version: 2.9.10 + No. of tool users (5 years) (usegalaxy.eu): 669 + No. of tool users (5 years) (usegalaxy.org): 1261 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1930 + No. of tool users (all time) (usegalaxy.eu): 669 + No. of tool users (all time) (usegalaxy.org): 1261 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1930 + Source: https://github.com/Illumina/strelka/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 112 + Tool usage (5 years) (usegalaxy.org): 417 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 529 + Tool usage (all time) (usegalaxy.eu): 112 + Tool usage (all time) (usegalaxy.org): 417 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 529 + ToolShed categories: + - Variant Analysis + ToolShed id: strelka + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 2 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: stringtie + Conda version: 2.2.3 + Date of first commit of the suite: '2019-09-05' + Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments + into potential transcripts. + EDAM operation: + - Transcriptome assembly + - RNA-Seq analysis + EDAM operation (no superclasses): + - Transcriptome assembly + - RNA-Seq analysis + EDAM topic: + - Transcriptomics + - RNA-seq + EDAM topic (no superclasses): + - Transcriptomics + Galaxy tool ids: + - stringtie + - stringtie_merge + Galaxy wrapper id: stringtie + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie + Galaxy wrapper version: 2.2.3 + No. of tool users (5 years) (usegalaxy.eu): 178677 + No. of tool users (5 years) (usegalaxy.org): 320780 + No. of tool users (5 years) (usegalaxy.org.au): 26375 + No. of tool users (5 years) - all main servers: 525832 + No. of tool users (all time) (usegalaxy.eu): 187728 + No. of tool users (all time) (usegalaxy.org): 407379 + No. of tool users (all time) (usegalaxy.org.au): 28921 + No. of tool users (all time) - all main servers: 624028 + Source: http://ccb.jhu.edu/software/stringtie/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4972 + Tool usage (5 years) (usegalaxy.org): 10825 + Tool usage (5 years) (usegalaxy.org.au): 1032 + Tool usage (5 years) - all main servers: 16829 + Tool usage (all time) (usegalaxy.eu): 5347 + Tool usage (all time) (usegalaxy.org): 15171 + Tool usage (all time) (usegalaxy.org.au): 1167 + Tool usage (all time) - all main servers: 21685 + ToolShed categories: + - Transcriptomics + ToolShed id: stringtie + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Fast and highly efficient assembler of RNA-Seq alignments + into potential transcripts. It uses a novel network flow algorithm as well as + an optional de novo assembly step to assemble and quantitate full-length transcripts + representing multiple splice variants for each gene locus. + bio.tool id: stringtie + bio.tool ids: + - stringtie + bio.tool name: StringTie +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: structure + Conda version: 2.3.4 + Date of first commit of the suite: '2017-09-22' + Description: for using multi-locus genotype data to investigate population structure. + EDAM operation: + - Genetic variation analysis + EDAM operation (no superclasses): + - Genetic variation analysis + EDAM topic: + - Population genetics + EDAM topic (no superclasses): + - Population genetics + Galaxy tool ids: + - structure + Galaxy wrapper id: structure + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure + Galaxy wrapper version: 2.3.4 + No. of tool users (5 years) (usegalaxy.eu): 2858 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2858 + No. of tool users (all time) (usegalaxy.eu): 3001 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3001 + Source: https://web.stanford.edu/group/pritchardlab/structure.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 118 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 118 + Tool usage (all time) (usegalaxy.eu): 123 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 123 + ToolShed categories: + - Phylogenetics + - Variant Analysis + ToolShed id: structure + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: The program structureis a free software package for using + multi-locus genotype data to investigate population structure. Its uses include + inferring the presence of distinct populations, assigning individuals to populations, + studying hybrid zones, identifying migrants and admixed individuals, and estimating + population allele frequencies in situations where many individuals are migrants + or admixed. + bio.tool id: structure + bio.tool ids: + - structure + bio.tool name: Structure +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: structureharvester + Conda version: 0.6.94 + Date of first commit of the suite: '2017-12-06' + Description: for parsing STRUCTURE outputs and for performing the Evanno method + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - structureharvester + Galaxy wrapper id: structureharvester + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester + Galaxy wrapper version: 0.6.94 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Phylogenetics + - Variant Analysis + ToolShed id: structureharvester + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: swiftlink + Conda version: '1.0' + Date of first commit of the suite: '2017-11-21' + Description: Parallel MCMC Linkage Analysis + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - swiftlink + Galaxy wrapper id: swift + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/ajm/swiftlink + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Variant Analysis + ToolShed id: swiftlink + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: clustalo + Conda version: 1.2.4 + Date of first commit of the suite: '2022-06-23' + Description: SynDivA was developed to analyze the diversity of synthetic libraries + of a Fibronectin domain. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - syndiva + Galaxy wrapper id: syndiva + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 30 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 30 + No. of tool users (all time) (usegalaxy.eu): 30 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 30 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Proteomics + ToolShed id: syndiva + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: pandas + Conda version: null + Date of first commit of the suite: '2019-08-28' + Description: Perform general-purpose table operations + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - table_compute + Galaxy wrapper id: table_compute + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute + Galaxy wrapper version: 1.2.4 + No. of tool users (5 years) (usegalaxy.eu): 216072 + No. of tool users (5 years) (usegalaxy.org): 12326 + No. of tool users (5 years) (usegalaxy.org.au): 16136 + No. of tool users (5 years) - all main servers: 244534 + No. of tool users (all time) (usegalaxy.eu): 216115 + No. of tool users (all time) (usegalaxy.org): 12326 + No. of tool users (all time) (usegalaxy.org.au): 16136 + No. of tool users (all time) - all main servers: 244577 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1811 + Tool usage (5 years) (usegalaxy.org): 1558 + Tool usage (5 years) (usegalaxy.org.au): 256 + Tool usage (5 years) - all main servers: 3625 + Tool usage (all time) (usegalaxy.eu): 1814 + Tool usage (all time) (usegalaxy.org): 1558 + Tool usage (all time) (usegalaxy.org.au): 256 + Tool usage (all time) - all main servers: 3628 + ToolShed categories: + - Text Manipulation + ToolShed id: table_compute + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: openjdk + Conda version: null + Date of first commit of the suite: '2016-05-05' + Description: Contains a tool that generates a frequency pileup of the 5' ends of + aligned reads in a BAM filerelative to reference points in a BED file. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tag_pileup_frequency + Galaxy wrapper id: tag_pileup_frequency + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 158 + No. of tool users (5 years) (usegalaxy.org): 722 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 880 + No. of tool users (all time) (usegalaxy.eu): 164 + No. of tool users (all time) (usegalaxy.org): 865 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1029 + Source: https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup + Status: To update + Tool usage (5 years) (usegalaxy.eu): 15 + Tool usage (5 years) (usegalaxy.org): 40 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 55 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 73 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 89 + ToolShed categories: + - Statistics + - SAM + - Genomic Interval Operations + ToolShed id: tag_pileup_frequency + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: tasmanian-mismatch + Conda version: 1.0.7 + Date of first commit of the suite: '2020-04-30' + Description: Analysis of positional mismatches + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tasmanian_mismatch + Galaxy wrapper id: tasmanian_mismatch + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch + Galaxy wrapper version: 1.0.7 + No. of tool users (5 years) (usegalaxy.eu): 4 + No. of tool users (5 years) (usegalaxy.org): 61 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 65 + No. of tool users (all time) (usegalaxy.eu): 4 + No. of tool users (all time) (usegalaxy.org): 61 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 65 + Source: https://github.com/nebiolabs/tasmanian-mismatch + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 7 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 7 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Sequence Analysis + ToolShed id: tasmanian_mismatch + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: taxonkit + Conda version: 0.17.0 + Date of first commit of the suite: '2024-07-26' + Description: TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit + EDAM operation: + - Formatting + - Data retrieval + EDAM operation (no superclasses): + - Formatting + - Data retrieval + EDAM topic: + - Taxonomy + - Biotechnology + - Ecology + EDAM topic (no superclasses): + - Taxonomy + - Biotechnology + - Ecology + Galaxy tool ids: + - name2taxid + - profile2cami + Galaxy wrapper id: taxonkit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit + Galaxy wrapper source: https://github.com/shenwei356/taxonkit + Galaxy wrapper version: 0.17.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://bioinf.shenwei.me/taxonkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: taxonkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: TaxonKit is a practical and efficient NCBI taxonomy toolkit. + bio.tool id: taxonkit + bio.tool ids: + - taxonkit + bio.tool name: TaxonKit +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rust-ncbitaxonomy + Conda version: 1.0.7 + Date of first commit of the suite: '2019-01-13' + Description: Filter RefSeq by taxonomy + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - taxonomy_filter_refseq + Galaxy wrapper id: taxonomy_filter_refseq + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc + Galaxy wrapper version: 0.3.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/pvanheus/ncbitaxonomy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + - Genome annotation + ToolShed id: taxonomy_filter_refseq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: krona + Conda version: 2.8.1 + Date of first commit of the suite: '2015-08-12' + Description: Krona pie chart from taxonomic profile + EDAM operation: + - Visualisation + EDAM operation (no superclasses): + - Visualisation + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - taxonomy_krona_chart + Galaxy wrapper id: taxonomy_krona_chart + Galaxy wrapper owner: crs4 + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart + Galaxy wrapper version: 2.7.1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 36069 + No. of tool users (5 years) (usegalaxy.org): 25255 + No. of tool users (5 years) (usegalaxy.org.au): 7949 + No. of tool users (5 years) - all main servers: 69273 + No. of tool users (all time) (usegalaxy.eu): 36922 + No. of tool users (all time) (usegalaxy.org): 30822 + No. of tool users (all time) (usegalaxy.org.au): 7949 + No. of tool users (all time) - all main servers: 75693 + Source: http://sourceforge.net/projects/krona/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5257 + Tool usage (5 years) (usegalaxy.org): 5066 + Tool usage (5 years) (usegalaxy.org.au): 1584 + Tool usage (5 years) - all main servers: 11907 + Tool usage (all time) (usegalaxy.eu): 5431 + Tool usage (all time) (usegalaxy.org): 5826 + Tool usage (all time) (usegalaxy.org.au): 1584 + Tool usage (all time) - all main servers: 12841 + ToolShed categories: + - Assembly + ToolShed id: taxonomy_krona_chart + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Krona creates interactive HTML5 charts of hierarchical data + (such as taxonomic abundance in a metagenome). + bio.tool id: krona + bio.tool ids: + - krona + bio.tool name: Krona +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: taxpasta + Conda version: 0.7.0 + Date of first commit of the suite: '2023-08-30' + Description: standardise taxonomic profiles + EDAM operation: + - Standardisation and normalisation + - Aggregation + - Formatting + - Conversion + EDAM operation (no superclasses): + - Standardisation and normalisation + - Aggregation + - Formatting + - Conversion + EDAM topic: + - Taxonomy + - Metagenomics + EDAM topic (no superclasses): + - Taxonomy + - Metagenomics + Galaxy tool ids: + - taxpasta + Galaxy wrapper id: taxpasta + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta + Galaxy wrapper source: https://github.com/taxprofiler/taxpasta + Galaxy wrapper version: 0.7.0 + No. of tool users (5 years) (usegalaxy.eu): 34 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 34 + No. of tool users (all time) (usegalaxy.eu): 34 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 34 + Source: https://taxpasta.readthedocs.io/en/latest/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Sequence Analysis + ToolShed id: taxpasta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: TAXonomic Profile Aggregation and STAndardisationThe main + purpose of taxpasta is to standardise taxonomic profiles created by a range of + bioinformatics tools. We call those tools taxonomic profilers. They each come + with their own particular tabular output format. Across the profilers, relative + abundances can be reported in read counts, fractions, or percentages, as well + as any number of additional columns with extra information. We therefore decided + to take the lessons learnt to heart and provide our own solution to deal with + this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, + output taxonomy identifiers and their integer counts. Taxpasta can not only standardise + profiles but also merge them across samples for the same profiler into a single + table. + bio.tool id: taxpasta + bio.tool ids: + - taxpasta + bio.tool name: taxpasta +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: tb-profiler + Conda version: 6.3.0 + Date of first commit of the suite: '2019-08-16' + Description: Processes M. tuberculosis sequence data to infer strain type and identify + known drug resistance markers. + EDAM operation: + - Antimicrobial resistance prediction + EDAM operation (no superclasses): + - Antimicrobial resistance prediction + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tb_profiler_profile + Galaxy wrapper id: tb-profiler + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler + Galaxy wrapper version: 6.2.1 + No. of tool users (5 years) (usegalaxy.eu): 6372 + No. of tool users (5 years) (usegalaxy.org): 7339 + No. of tool users (5 years) (usegalaxy.org.au): 6966 + No. of tool users (5 years) - all main servers: 20677 + No. of tool users (all time) (usegalaxy.eu): 6395 + No. of tool users (all time) (usegalaxy.org): 7339 + No. of tool users (all time) (usegalaxy.org.au): 6966 + No. of tool users (all time) - all main servers: 20700 + Source: https://github.com/jodyphelan/TBProfiler + Status: To update + Tool usage (5 years) (usegalaxy.eu): 372 + Tool usage (5 years) (usegalaxy.org): 378 + Tool usage (5 years) (usegalaxy.org.au): 154 + Tool usage (5 years) - all main servers: 904 + Tool usage (all time) (usegalaxy.eu): 379 + Tool usage (all time) (usegalaxy.org): 378 + Tool usage (all time) (usegalaxy.org.au): 154 + Tool usage (all time) - all main servers: 911 + ToolShed categories: + - Sequence Analysis + ToolShed id: tbprofiler + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool for drug resistance prediction from _M. tuberculosis_ + genomic data (sequencing reads, alignments or variants). + bio.tool id: tb-profiler + bio.tool ids: + - tb-profiler + bio.tool name: tb-profiler +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: tb_variant_filter + Conda version: 0.4.0 + Date of first commit of the suite: '2019-10-03' + Description: M. tuberculosis H37Rv VCF filter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tb_variant_filter + Galaxy wrapper id: tb_variant_filter + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter + Galaxy wrapper source: https://github.com/COMBAT-TB/tb_variant_filter + Galaxy wrapper version: 0.4.0 + No. of tool users (5 years) (usegalaxy.eu): 22977 + No. of tool users (5 years) (usegalaxy.org): 3888 + No. of tool users (5 years) (usegalaxy.org.au): 3611 + No. of tool users (5 years) - all main servers: 30476 + No. of tool users (all time) (usegalaxy.eu): 22977 + No. of tool users (all time) (usegalaxy.org): 3888 + No. of tool users (all time) (usegalaxy.org.au): 3611 + No. of tool users (all time) - all main servers: 30476 + Source: https://github.com/COMBAT-TB/tb_variant_filter + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 461 + Tool usage (5 years) (usegalaxy.org): 274 + Tool usage (5 years) (usegalaxy.org.au): 80 + Tool usage (5 years) - all main servers: 815 + Tool usage (all time) (usegalaxy.eu): 461 + Tool usage (all time) (usegalaxy.org): 274 + Tool usage (all time) (usegalaxy.org.au): 80 + Tool usage (all time) - all main servers: 815 + ToolShed categories: + - Variant Analysis + ToolShed id: tb_variant_filter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bcbiogff + Conda version: 0.6.6 + Date of first commit of the suite: '2020-07-07' + Description: Table to GFF3 + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tbl2gff3 + Galaxy wrapper id: tbl2gff3 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 + Galaxy wrapper version: '1.2' + No. of tool users (5 years) (usegalaxy.eu): 1941 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 463 + No. of tool users (5 years) - all main servers: 2404 + No. of tool users (all time) (usegalaxy.eu): 1941 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 463 + No. of tool users (all time) - all main servers: 2404 + Source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 + Status: To update + Tool usage (5 years) (usegalaxy.eu): 466 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 112 + Tool usage (5 years) - all main servers: 578 + Tool usage (all time) (usegalaxy.eu): 466 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 112 + Tool usage (all time) - all main servers: 578 + ToolShed categories: + - Convert Formats + - Sequence Analysis + ToolShed id: tbl2gff3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: tbvcfreport + Conda version: 1.0.1 + Date of first commit of the suite: '2019-08-29' + Description: Generate HTML report from SnpEff M.tuberculosis VCF(s) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tbvcfreport + Galaxy wrapper id: tbvcfreport + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 2955 + No. of tool users (5 years) (usegalaxy.org): 6090 + No. of tool users (5 years) (usegalaxy.org.au): 2347 + No. of tool users (5 years) - all main servers: 11392 + No. of tool users (all time) (usegalaxy.eu): 2955 + No. of tool users (all time) (usegalaxy.org): 6090 + No. of tool users (all time) (usegalaxy.org.au): 2347 + No. of tool users (all time) - all main servers: 11392 + Source: https://github.com/COMBAT-TB/tbvcfreport + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 335 + Tool usage (5 years) (usegalaxy.org): 348 + Tool usage (5 years) (usegalaxy.org.au): 72 + Tool usage (5 years) - all main servers: 755 + Tool usage (all time) (usegalaxy.eu): 335 + Tool usage (all time) (usegalaxy.org): 348 + Tool usage (all time) (usegalaxy.org.au): 72 + Tool usage (all time) - all main servers: 755 + ToolShed categories: + - Variant Analysis + ToolShed id: tbvcfreport + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: samtools + Conda version: '1.21' + Date of first commit of the suite: '2022-08-08' + Description: Transposable element insertions finder + EDAM operation: + - Genome indexing + - Variant calling + - PCR primer design + EDAM operation (no superclasses): + - Genome indexing + - Variant calling + - PCR primer design + EDAM topic: + - Sequencing + - Mobile genetic elements + - Workflows + - Evolutionary biology + - Genetic variation + EDAM topic (no superclasses): + - Sequencing + - Mobile genetic elements + - Workflows + - Evolutionary biology + - Genetic variation + Galaxy tool ids: + - te_finder + Galaxy wrapper id: te_finder + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 203 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 203 + No. of tool users (all time) (usegalaxy.eu): 203 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 203 + Source: https://github.com/VistaSohrab/TEfinder + Status: To update + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 20 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 20 + ToolShed categories: + - Sequence Analysis + ToolShed id: te_finder + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: A Bioinformatics Pipeline for Detecting New Transposable Element + Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for + detecting novel transposable element insertions.TEfinder uses discordant reads + to detect novel transposable element insertion events in paired-end sample sequencing + data. + bio.tool id: tefinder + bio.tool ids: + - tefinder + bio.tool name: TEfinder +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: telescope + Conda version: 1.0.3 + Date of first commit of the suite: '2019-09-03' + Description: Single locus resolution of Transposable ELEment expression. + EDAM operation: + - Essential dynamics + - Sequence trimming + - RNA-Seq quantification + - Expression analysis + - Read mapping + EDAM operation (no superclasses): + - Essential dynamics + - Sequence trimming + - RNA-Seq quantification + - Expression analysis + - Read mapping + EDAM topic: + - RNA-Seq + - Transcriptomics + - Mapping + - Gene transcripts + - Sequence assembly + EDAM topic (no superclasses): + - RNA-Seq + - Transcriptomics + - Mapping + - Gene transcripts + - Sequence assembly + Galaxy tool ids: + - telescope_assign + Galaxy wrapper id: telescope + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope + Galaxy wrapper version: 1.0.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/mlbendall/telescope/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Genome annotation + ToolShed id: telescope_assign + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: 'Telescope is a tool for the characterization of the retrotranscriptome + by accurate estimation of transposable element expression and the quantification + of transposable element expression using RNA-seq.It can be used for Statistical + Performance of TE Quantification Methods.All scripts needed to examine the sensitivity + and biases of computational approaches for quantifying TE expression: 1) unique + counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, + and 7) Telescope.' + bio.tool id: Telescope-expression + bio.tool ids: + - Telescope-expression + bio.tool name: Telescope +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: tetranscripts + Conda version: 2.2.3 + Date of first commit of the suite: '2020-04-10' + Description: The TEToolkit suite improves the bioinformatic analysis of repetitive + sequences, particularly transposable elements, in order to elucidate novel (and + previously ignored) biological insights of their functions in development and + diseases. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tetoolkit_tetranscripts + Galaxy wrapper id: tetoolkit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit + Galaxy wrapper source: https://github.com/mhammell-laboratory/TEtranscripts + Galaxy wrapper version: 2.2.3 + No. of tool users (5 years) (usegalaxy.eu): 1013 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 70 + No. of tool users (5 years) - all main servers: 1083 + No. of tool users (all time) (usegalaxy.eu): 1013 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 70 + No. of tool users (all time) - all main servers: 1083 + Source: http://hammelllab.labsites.cshl.edu/software/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 74 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 78 + Tool usage (all time) (usegalaxy.eu): 74 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 78 + ToolShed categories: + - Sequence Analysis + ToolShed id: tetoolkit + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: tetyper + Conda version: '1.1' + Date of first commit of the suite: '2019-11-23' + Description: Type a specific transposable element (TE) of interest from paired-end + sequencing data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tetyper + Galaxy wrapper id: tetyper + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper + Galaxy wrapper version: '1.1' + No. of tool users (5 years) (usegalaxy.eu): 106 + No. of tool users (5 years) (usegalaxy.org): 155 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 261 + No. of tool users (all time) (usegalaxy.eu): 106 + No. of tool users (all time) (usegalaxy.org): 155 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 261 + Source: https://github.com/aesheppard/TETyper + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 47 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 63 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 47 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 63 + ToolShed categories: + - Sequence Analysis + ToolShed id: tetyper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 0 + Conda id: tn93 + Conda version: 1.0.14 + Date of first commit of the suite: '2018-06-06' + Description: Compute distances between sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tn93_readreduce + - tn93 + - tn93_cluster + - tn93_filter + Galaxy wrapper id: tn93 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ + Galaxy wrapper version: 1.0.14 + No. of tool users (5 years) (usegalaxy.eu): 1915 + No. of tool users (5 years) (usegalaxy.org): 1972 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3887 + No. of tool users (all time) (usegalaxy.eu): 1915 + No. of tool users (all time) (usegalaxy.org): 1972 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3887 + Source: https://github.com/veg/tn93/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 42 + Tool usage (5 years) (usegalaxy.org): 225 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 267 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 225 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 267 + ToolShed categories: + - Sequence Analysis + ToolShed id: tn93 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 2 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 2 + UseGalaxy.or: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: tooldistillator + Conda version: 0.9.1 + Date of first commit of the suite: '2024-04-30' + Description: ToolDistillator extract and aggregate information from different tool + outputs to JSON parsable files + EDAM operation: + - Data handling + - Parsing + EDAM operation (no superclasses): + - Parsing + EDAM topic: + - Microbiology + - Bioinformatics + - Sequence analysis + EDAM topic (no superclasses): + - Microbiology + - Bioinformatics + - Sequence analysis + Galaxy tool ids: + - tooldistillator + - tooldistillator_summarize + Galaxy wrapper id: tooldistillator + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator + Galaxy wrapper version: 0.9.1 + No. of tool users (5 years) (usegalaxy.eu): 65 + No. of tool users (5 years) (usegalaxy.org): 6 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 71 + No. of tool users (all time) (usegalaxy.eu): 65 + No. of tool users (all time) (usegalaxy.org): 6 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 71 + Source: https://gitlab.com/ifb-elixirfr/abromics/tooldistillator + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 5 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 14 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 5 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 14 + ToolShed categories: + - Sequence Analysis + ToolShed id: tooldistillator + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: ToolDistillator is a tool to extract information from output + files of specific tools, expose it as JSON files, and aggregate over several tools.It + can produce both a single file to each tool or a summarized file from a set of + reports. + bio.tool id: tooldistillator + bio.tool ids: + - tooldistillator + bio.tool name: ToolDistillator +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: tracegroomer + Conda version: 0.1.4 + Date of first commit of the suite: '2024-03-28' + Description: TraceGroomer is a solution for formatting and normalising Tracer metabolomics + given file(s), to produce the .csv files which are ready for DIMet tool. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tracegroomer + Galaxy wrapper id: tracegroomer + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer + Galaxy wrapper version: 0.1.4 + No. of tool users (5 years) (usegalaxy.eu): 7 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7 + No. of tool users (all time) (usegalaxy.eu): 7 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7 + Source: https://github.com/cbib/TraceGroomer + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: tracy + Conda version: 0.7.8 + Date of first commit of the suite: '2021-10-12' + Description: null + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tracy_align + - tracy_assemble + - tracy_basecall + - tracy_decompose + Galaxy wrapper id: tracy + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy + Galaxy wrapper version: 0.6.1 + No. of tool users (5 years) (usegalaxy.eu): 3314 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 3314 + No. of tool users (all time) (usegalaxy.eu): 3314 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 3314 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 124 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 124 + Tool usage (all time) (usegalaxy.eu): 124 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 124 + ToolShed categories: [] + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: transdecoder + Conda version: 5.7.1 + Date of first commit of the suite: '2015-11-09' + Description: TransDecoder finds coding regions within transcripts + EDAM operation: + - Coding region prediction + - de Novo sequencing + - De-novo assembly + EDAM operation (no superclasses): + - Coding region prediction + - de Novo sequencing + - De-novo assembly + EDAM topic: + - Genomics + - Gene transcripts + - RNA-Seq + - Gene expression + - Sequence assembly + - Whole genome sequencing + EDAM topic (no superclasses): + - Genomics + - Gene transcripts + - RNA-Seq + - Gene expression + - Sequence assembly + - Whole genome sequencing + Galaxy tool ids: + - transdecoder + Galaxy wrapper id: transdecoder + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder + Galaxy wrapper version: 5.5.0 + No. of tool users (5 years) (usegalaxy.eu): 5964 + No. of tool users (5 years) (usegalaxy.org): 5450 + No. of tool users (5 years) (usegalaxy.org.au): 2610 + No. of tool users (5 years) - all main servers: 14024 + No. of tool users (all time) (usegalaxy.eu): 6418 + No. of tool users (all time) (usegalaxy.org): 5450 + No. of tool users (all time) (usegalaxy.org.au): 2796 + No. of tool users (all time) - all main servers: 14664 + Source: https://transdecoder.github.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 944 + Tool usage (5 years) (usegalaxy.org): 1066 + Tool usage (5 years) (usegalaxy.org.au): 317 + Tool usage (5 years) - all main servers: 2327 + Tool usage (all time) (usegalaxy.eu): 970 + Tool usage (all time) (usegalaxy.org): 1066 + Tool usage (all time) (usegalaxy.org.au): 344 + Tool usage (all time) - all main servers: 2380 + ToolShed categories: + - Transcriptomics + - RNA + ToolShed id: transdecoder + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: TransDecoder identifies candidate coding regions within transcript + sequences, such as those generated by de novo RNA-Seq transcript assembly using + Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat + and Cufflinks. + bio.tool id: TransDecoder + bio.tool ids: + - TransDecoder + bio.tool name: TransDecoder +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: transit + Conda version: 3.2.3 + Date of first commit of the suite: '2019-03-01' + Description: TRANSIT + EDAM operation: + - Transposon prediction + EDAM operation (no superclasses): + - Transposon prediction + EDAM topic: + - DNA + - Sequencing + - Mobile genetic elements + EDAM topic (no superclasses): + - DNA + - Sequencing + - Mobile genetic elements + Galaxy tool ids: + - gff_to_prot + - transit_gumbel + - transit_hmm + - transit_resampling + - transit_tn5gaps + Galaxy wrapper id: transit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ + Galaxy wrapper version: 3.0.2 + No. of tool users (5 years) (usegalaxy.eu): 1039 + No. of tool users (5 years) (usegalaxy.org): 2672 + No. of tool users (5 years) (usegalaxy.org.au): 358 + No. of tool users (5 years) - all main servers: 4069 + No. of tool users (all time) (usegalaxy.eu): 1039 + No. of tool users (all time) (usegalaxy.org): 3349 + No. of tool users (all time) (usegalaxy.org.au): 358 + No. of tool users (all time) - all main servers: 4746 + Source: https://github.com/mad-lab/transit/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 189 + Tool usage (5 years) (usegalaxy.org): 467 + Tool usage (5 years) (usegalaxy.org.au): 47 + Tool usage (5 years) - all main servers: 703 + Tool usage (all time) (usegalaxy.eu): 189 + Tool usage (all time) (usegalaxy.org): 485 + Tool usage (all time) (usegalaxy.org.au): 47 + Tool usage (all time) - all main servers: 721 + ToolShed categories: + - Genome annotation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: A tool for the analysis of Tn-Seq data. It provides an easy + to use graphical interface and access to three different analysis methods that + allow the user to determine essentiality in a single condition as well as between + conditions. + bio.tool id: transit + bio.tool ids: + - transit + bio.tool name: TRANSIT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: transtermhp + Conda version: '2.09' + Date of first commit of the suite: '2015-10-08' + Description: Finds rho-independent transcription terminators in bacterial genomes + EDAM operation: + - Transcriptional regulatory element prediction + EDAM operation (no superclasses): + - Transcriptional regulatory element prediction + EDAM topic: + - Transcription factors and regulatory sites + EDAM topic (no superclasses): + - Transcription factors and regulatory sites + Galaxy tool ids: + - transtermhp + Galaxy wrapper id: transtermhp + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 250 + No. of tool users (5 years) (usegalaxy.org): 174 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 424 + No. of tool users (all time) (usegalaxy.eu): 254 + No. of tool users (all time) (usegalaxy.org): 174 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 428 + Source: https://transterm.cbcb.umd.edu + Status: To update + Tool usage (5 years) (usegalaxy.eu): 31 + Tool usage (5 years) (usegalaxy.org): 45 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 76 + Tool usage (all time) (usegalaxy.eu): 31 + Tool usage (all time) (usegalaxy.org): 45 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 76 + ToolShed categories: + - Sequence Analysis + ToolShed id: transtermhp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: TransTermHP finds rho-independent transcription terminators + in bacterial genomes. Each terminator found by the program is assigned a confidence + value that estimates its probability of being a true terminator + bio.tool id: transtermhp + bio.tool ids: + - transtermhp + bio.tool name: TransTermHP +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: trimmomatic + Conda version: '0.39' + Date of first commit of the suite: '2024-01-03' + Description: A flexible read trimming tool for Illumina NGS data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - trimmomatic + Galaxy wrapper id: trimmomatic + Galaxy wrapper owner: pjbriggs + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic + Galaxy wrapper version: '0.39' + No. of tool users (5 years) (usegalaxy.eu): 352353 + No. of tool users (5 years) (usegalaxy.org): 632385 + No. of tool users (5 years) (usegalaxy.org.au): 125340 + No. of tool users (5 years) - all main servers: 1110078 + No. of tool users (all time) (usegalaxy.eu): 383014 + No. of tool users (all time) (usegalaxy.org): 839058 + No. of tool users (all time) (usegalaxy.org.au): 139097 + No. of tool users (all time) - all main servers: 1361169 + Source: http://www.usadellab.org/cms/?page=trimmomatic + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 14547 + Tool usage (5 years) (usegalaxy.org): 39323 + Tool usage (5 years) (usegalaxy.org.au): 5268 + Tool usage (5 years) - all main servers: 59138 + Tool usage (all time) (usegalaxy.eu): 15408 + Tool usage (all time) (usegalaxy.org): 49850 + Tool usage (all time) (usegalaxy.org.au): 5975 + Tool usage (all time) - all main servers: 71233 + ToolShed categories: + - Fastq Manipulation + ToolShed id: trimmomatic + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 1 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 13 + Available on UseGalaxy.fr: 13 + Available on UseGalaxy.org (Main): 9 + Available on UseGalaxy.org.au: 13 + Conda id: trinity + Conda version: 2.15.2 + Date of first commit of the suite: '2019-11-13' + Description: Trinity represents a method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq + EDAM operation: + - Transcriptome assembly + EDAM operation (no superclasses): + - Transcriptome assembly + EDAM topic: + - Transcriptomics + - Gene expression + - Gene transcripts + EDAM topic (no superclasses): + - Transcriptomics + - Gene transcripts + Galaxy tool ids: + - trinity_abundance_estimates_to_matrix + - trinity_align_and_estimate_abundance + - trinity_analyze_diff_expr + - trinity_contig_exn50_statistic + - trinity_define_clusters_by_cutting_tree + - describe_samples + - trinity_filter_low_expr_transcripts + - trinity_gene_to_trans_map + - trinity_run_de_analysis + - trinity_samples_qccheck + - trinity_super_transcripts + - trinity + - trinity_stats + Galaxy wrapper id: trinity + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity + Galaxy wrapper version: 2.15.1 + No. of tool users (5 years) (usegalaxy.eu): 35698 + No. of tool users (5 years) (usegalaxy.org): 44509 + No. of tool users (5 years) (usegalaxy.org.au): 21883 + No. of tool users (5 years) - all main servers: 102090 + No. of tool users (all time) (usegalaxy.eu): 39132 + No. of tool users (all time) (usegalaxy.org): 44509 + No. of tool users (all time) (usegalaxy.org.au): 23889 + No. of tool users (all time) - all main servers: 107530 + Source: https://github.com/trinityrnaseq/trinityrnaseq + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4376 + Tool usage (5 years) (usegalaxy.org): 6714 + Tool usage (5 years) (usegalaxy.org.au): 1924 + Tool usage (5 years) - all main servers: 13014 + Tool usage (all time) (usegalaxy.eu): 4632 + Tool usage (all time) (usegalaxy.org): 6714 + Tool usage (all time) (usegalaxy.org.au): 2070 + Tool usage (all time) - all main servers: 13416 + ToolShed categories: + - Transcriptomics + - RNA + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 11 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 1 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 11 + Tools available on UseGalaxy.cz: 13 + Tools available on UseGalaxy.eu: 13 + Tools available on UseGalaxy.fr: 13 + Tools available on UseGalaxy.no: 12 + Tools available on UseGalaxy.org (Main): 9 + Tools available on UseGalaxy.org.au: 13 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 11 + UseGalaxy.cz: 13 + UseGalaxy.eu: 13 + UseGalaxy.fr: 1 + UseGalaxy.no: 12 + UseGalaxy.or: 13 + biii: null + bio.tool description: Trinity is a transcriptome assembler which relies on three + different tools, inchworm an assembler, chrysalis which pools contigs and butterfly + which amongst others compacts a graph resulting from butterfly with reads. + bio.tool id: trinity + bio.tool ids: + - trinity + bio.tool name: Trinity +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: trinotate + Conda version: 4.0.2 + Date of first commit of the suite: '2016-11-15' + Description: Trinotate is a comprehensive annotation suite designed for automatic + functional annotation of de novo transcriptomes. + EDAM operation: + - Gene functional annotation + EDAM operation (no superclasses): + - Gene functional annotation + EDAM topic: + - Gene expression + - Transcriptomics + EDAM topic (no superclasses): + - Transcriptomics + Galaxy tool ids: + - trinotate + Galaxy wrapper id: trinotate + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate + Galaxy wrapper version: 3.2.2 + No. of tool users (5 years) (usegalaxy.eu): 1968 + No. of tool users (5 years) (usegalaxy.org): 1825 + No. of tool users (5 years) (usegalaxy.org.au): 862 + No. of tool users (5 years) - all main servers: 4655 + No. of tool users (all time) (usegalaxy.eu): 2080 + No. of tool users (all time) (usegalaxy.org): 1825 + No. of tool users (all time) (usegalaxy.org.au): 1060 + No. of tool users (all time) - all main servers: 4965 + Source: https://trinotate.github.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 374 + Tool usage (5 years) (usegalaxy.org): 527 + Tool usage (5 years) (usegalaxy.org.au): 161 + Tool usage (5 years) - all main servers: 1062 + Tool usage (all time) (usegalaxy.eu): 390 + Tool usage (all time) (usegalaxy.org): 527 + Tool usage (all time) (usegalaxy.org.au): 195 + Tool usage (all time) - all main servers: 1112 + ToolShed categories: + - Transcriptomics + - RNA + ToolShed id: trinotate + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Comprehensive annotation suite designed for automatic functional + annotation of transcriptomes, particularly de novo assembled transcriptomes, from + model or non-model organisms. + bio.tool id: trinotate + bio.tool ids: + - trinotate + bio.tool name: Trinotate +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 5 + Conda id: trycycler + Conda version: 0.5.5 + Date of first commit of the suite: '2021-02-11' + Description: Trycycler toolkit wrappers + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - trycycler_cluster + - trycycler_consensus + - trycycler_partition + - trycycler_reconcile_msa + - trycycler_subsample + Galaxy wrapper id: trycycler + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler + Galaxy wrapper version: 0.5.5 + No. of tool users (5 years) (usegalaxy.eu): 14681 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 4488 + No. of tool users (5 years) - all main servers: 19169 + No. of tool users (all time) (usegalaxy.eu): 14681 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 4488 + No. of tool users (all time) - all main servers: 19169 + Source: https://github.com/rrwick/Trycycler + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 265 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 147 + Tool usage (5 years) - all main servers: 412 + Tool usage (all time) (usegalaxy.eu): 265 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 147 + Tool usage (all time) - all main servers: 412 + ToolShed categories: + - Assembly + ToolShed id: trycycler + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 5 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: tsebra + Conda version: 1.1.2.5 + Date of first commit of the suite: '2023-10-19' + Description: This tool has been developed to combine BRAKER predictions. + EDAM operation: + - Homology-based gene prediction + - Alternative splicing prediction + EDAM operation (no superclasses): + - Homology-based gene prediction + - Alternative splicing prediction + EDAM topic: + - Gene expression + - RNA-Seq + - Gene transcripts + - Model organisms + EDAM topic (no superclasses): + - Gene expression + - RNA-Seq + - Gene transcripts + - Model organisms + Galaxy tool ids: + - tsebra + Galaxy wrapper id: tsebra + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra + Galaxy wrapper version: 1.1.2.5 + No. of tool users (5 years) (usegalaxy.eu): 17 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 17 + No. of tool users (all time) (usegalaxy.eu): 17 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 17 + Source: https://github.com/Gaius-Augustus/TSEBRA + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - Genome annotation + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: TSEBRA is a combiner tool that selects transcripts from gene + predictions based on the support by extrisic evidence in form of introns and start/stop + codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase + their accuracies. + bio.tool id: tsebra + bio.tool ids: + - tsebra + bio.tool name: TSEBRA +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: r-rtsne + Conda version: '0.13' + Date of first commit of the suite: '2017-05-26' + Description: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tsne + Galaxy wrapper id: tsne + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne + Galaxy wrapper version: 0.0.2 + No. of tool users (5 years) (usegalaxy.eu): 255 + No. of tool users (5 years) (usegalaxy.org): 281 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 536 + No. of tool users (all time) (usegalaxy.eu): 379 + No. of tool users (all time) (usegalaxy.org): 281 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 660 + Source: https://cran.r-project.org/web/packages/Rtsne/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 31 + Tool usage (5 years) (usegalaxy.org): 64 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 95 + Tool usage (all time) (usegalaxy.eu): 37 + Tool usage (all time) (usegalaxy.org): 64 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 101 + ToolShed categories: + - Text Manipulation + ToolShed id: tsne + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-tximport + Conda version: 1.30.0 + Date of first commit of the suite: '2019-11-27' + Description: Wrapper for the Bioconductor package tximport + EDAM operation: + - Pathway or network analysis + - Formatting + - RNA-Seq analysis + EDAM operation (no superclasses): + - Pathway or network analysis + - Formatting + - RNA-Seq analysis + EDAM topic: + - Transcriptomics + - Gene transcripts + - Workflows + EDAM topic (no superclasses): + - Transcriptomics + - Gene transcripts + - Workflows + Galaxy tool ids: + - tximport + Galaxy wrapper id: tximport + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport + Galaxy wrapper version: 1.30.0 + No. of tool users (5 years) (usegalaxy.eu): 1802 + No. of tool users (5 years) (usegalaxy.org): 6963 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 8765 + No. of tool users (all time) (usegalaxy.eu): 1802 + No. of tool users (all time) (usegalaxy.org): 6963 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8765 + Source: http://bioconductor.org/packages/tximport/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 225 + Tool usage (5 years) (usegalaxy.org): 904 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1129 + Tool usage (all time) (usegalaxy.eu): 225 + Tool usage (all time) (usegalaxy.org): 904 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1129 + ToolShed categories: + - Transcriptomics + ToolShed id: tximport + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: An R/Bioconductor package that imports transcript-level abundance, + estimated counts and transcript lengths, and summarizes into matrices for use + with downstream gene-level analysis packages. + bio.tool id: tximport + bio.tool ids: + - tximport + bio.tool name: tximport +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ucsc-blat + Conda version: '469' + Date of first commit of the suite: '2017-05-17' + Description: Standalone blat sequence search command line tool + EDAM operation: + - Sequence alignment + EDAM operation (no superclasses): + - Sequence alignment + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - ucsc_blat + Galaxy wrapper id: ucsc_blat + Galaxy wrapper owner: yating-l + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ + Galaxy wrapper version: '469' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://genome.ucsc.edu/goldenPath/help/blatSpec.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: ucsc_blat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 1 + biii: null + bio.tool description: Fast, accurate spliced alignment of DNA sequences. + bio.tool id: blat + bio.tool ids: + - blat + bio.tool name: BLAT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: ucsc-fasplit + Conda version: '469' + Date of first commit of the suite: '2017-09-08' + Description: faSplit is a tool to split a single FASTA file into several files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - fasplit + Galaxy wrapper id: fasplit + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit + Galaxy wrapper version: '469' + No. of tool users (5 years) (usegalaxy.eu): 3278 + No. of tool users (5 years) (usegalaxy.org): 6144 + No. of tool users (5 years) (usegalaxy.org.au): 1139 + No. of tool users (5 years) - 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UCSC_Genome_Browser_Utilities + bio.tool name: UCSC Genome Browser Utilities +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: ucsc-fatovcf + Conda version: '448' + Date of first commit of the suite: '2023-01-11' + Description: Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide + diffs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - fatovcf + Galaxy wrapper id: fatovcf + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf + Galaxy wrapper version: '448' + No. of tool users (5 years) (usegalaxy.eu): 385 + No. of tool users (5 years) (usegalaxy.org): 587 + No. of tool users (5 years) (usegalaxy.org.au): 58 + No. of tool users (5 years) - all main servers: 1030 + No. of tool users (all time) (usegalaxy.eu): 385 + No. of tool users (all time) (usegalaxy.org): 587 + No. of tool users (all time) (usegalaxy.org.au): 58 + No. of tool users (all time) - all main servers: 1030 + Source: http://hgdownload.cse.ucsc.edu/admin/exe/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 46 + Tool usage (5 years) (usegalaxy.org): 107 + Tool usage (5 years) (usegalaxy.org.au): 5 + Tool usage (5 years) - all main servers: 158 + Tool usage (all time) (usegalaxy.eu): 46 + Tool usage (all time) (usegalaxy.org): 107 + Tool usage (all time) (usegalaxy.org.au): 5 + Tool usage (all time) - all main servers: 158 + ToolShed categories: + - Convert Formats + ToolShed id: ucsc_fatovcf + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Utilities for handling sequences and assemblies from the UCSC + Genome Browser project. + bio.tool id: UCSC_Genome_Browser_Utilities + bio.tool ids: + - UCSC_Genome_Browser_Utilities + bio.tool name: UCSC Genome Browser Utilities +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: ucsc-maftoaxt + Conda version: '469' + Date of first commit of the suite: '2024-07-30' + Description: Convert dataset from MAF to axt format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - maftoaxt + Galaxy wrapper id: maftoaxt + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt + Galaxy wrapper version: '469' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://hgdownload.cse.ucsc.edu/admin/exe/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Convert Formats + ToolShed id: ucsc_maftoaxt + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Utilities for handling sequences and assemblies from the UCSC + Genome Browser project. + bio.tool id: UCSC_Genome_Browser_Utilities + bio.tool ids: + - UCSC_Genome_Browser_Utilities + bio.tool name: UCSC Genome Browser Utilities +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: ucsc-twobittofa + Conda version: '469' + Date of first commit of the suite: '2016-08-19' + Description: twoBitToFa is a tool to convert all or part of .2bit file to FASTA + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - ucsc-twobittofa + Galaxy wrapper id: twobittofa + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa + Galaxy wrapper version: '469' + No. of tool users (5 years) (usegalaxy.eu): 413 + No. of tool users (5 years) (usegalaxy.org): 441 + No. of tool users (5 years) (usegalaxy.org.au): 21 + No. of tool users (5 years) - 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UCSC_Genome_Browser_Utilities + bio.tool name: UCSC Genome Browser Utilities +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: ucsc-axtchain + Conda version: '469' + Date of first commit of the suite: '2024-08-26' + Description: Chain together genome alignments + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - ucsc_axtchain + Galaxy wrapper id: ucsc_axtchain + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain + Galaxy wrapper version: '469' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - 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UCSC_Genome_Browser_Utilities + bio.tool name: UCSC Genome Browser Utilities +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: ucsc-axttomaf + Conda version: '469' + Date of first commit of the suite: '2024-08-27' + Description: Convert dataset from axt to MAF format. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - ucsc_axtomaf + Galaxy wrapper id: ucsc_axttomaf + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf + Galaxy wrapper version: '469' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - 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UCSC_Genome_Browser_Utilities + bio.tool name: UCSC Genome Browser Utilities +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: umi_tools + Conda version: 1.1.5 + Date of first commit of the suite: '2021-07-15' + Description: UMI-tools extract - Extract UMIs from fastq + EDAM operation: + - Sequencing quality control + EDAM operation (no superclasses): + - Sequencing quality control + EDAM topic: + - NGS + - Sequence sites, features and motifs + - Quality affairs + EDAM topic (no superclasses): + - Sequence sites, features and motifs + - Quality affairs + Galaxy tool ids: + - umi_tools_count + - umi_tools_dedup + - umi_tools_extract + - umi_tools_group + - umi_tools_whitelist + Galaxy wrapper id: umi_tools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 55050 + No. of tool users (5 years) (usegalaxy.org): 9001 + No. of tool users (5 years) (usegalaxy.org.au): 12444 + No. of tool users (5 years) - all main servers: 76495 + No. of tool users (all time) (usegalaxy.eu): 68123 + No. of tool users (all time) (usegalaxy.org): 9001 + No. of tool users (all time) (usegalaxy.org.au): 12444 + No. of tool users (all time) - all main servers: 89568 + Source: https://github.com/CGATOxford/UMI-tools + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1090 + Tool usage (5 years) (usegalaxy.org): 906 + Tool usage (5 years) (usegalaxy.org.au): 187 + Tool usage (5 years) - all main servers: 2183 + Tool usage (all time) (usegalaxy.eu): 1223 + Tool usage (all time) (usegalaxy.org): 906 + Tool usage (all time) (usegalaxy.org.au): 187 + Tool usage (all time) - all main servers: 2316 + ToolShed categories: + - Sequence Analysis + - Transcriptomics + - Single Cell + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 5 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: Tools for handling Unique Molecular Identifiers in NGS data + sets. + bio.tool id: umi-tools + bio.tool ids: + - umi-tools + bio.tool name: UMI-tools +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: unicycler + Conda version: 0.5.1 + Date of first commit of the suite: '2018-08-28' + Description: Unicycler is a hybrid assembly pipeline for bacterial genomes. + EDAM operation: + - Genome assembly + - Aggregation + EDAM operation (no superclasses): + - Genome assembly + - Aggregation + EDAM topic: + - Microbiology + - Genomics + - Sequencing + - Sequence assembly + EDAM topic (no superclasses): + - Microbiology + - Genomics + - Sequencing + - Sequence assembly + Galaxy tool ids: + - unicycler + Galaxy wrapper id: unicycler + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler + Galaxy wrapper version: 0.5.1 + No. of tool users (5 years) (usegalaxy.eu): 74120 + No. of tool users (5 years) (usegalaxy.org): 64946 + No. of tool users (5 years) (usegalaxy.org.au): 19516 + No. of tool users (5 years) - all main servers: 158582 + No. of tool users (all time) (usegalaxy.eu): 77648 + No. of tool users (all time) (usegalaxy.org): 90075 + No. of tool users (all time) (usegalaxy.org.au): 20422 + No. of tool users (all time) - all main servers: 188145 + Source: https://github.com/rrwick/Unicycler + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 3798 + Tool usage (5 years) (usegalaxy.org): 5451 + Tool usage (5 years) (usegalaxy.org.au): 2010 + Tool usage (5 years) - all main servers: 11259 + Tool usage (all time) (usegalaxy.eu): 3963 + Tool usage (all time) (usegalaxy.org): 7380 + Tool usage (all time) (usegalaxy.org.au): 2080 + Tool usage (all time) - all main servers: 13423 + ToolShed categories: + - Assembly + ToolShed id: unicycler + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A tool for assembling bacterial genomes from a combination + of short (2nd generation) and long (3rd generation) sequencing reads. + bio.tool id: unicycler + bio.tool ids: + - unicycler + bio.tool name: Unicycler +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: usher + Conda version: 0.6.3 + Date of first commit of the suite: '2021-05-11' + Description: UShER toolkit wrappers + EDAM operation: + - Classification + - Phylogenetic tree visualisation + - Phylogenetic inference (from molecular sequences) + EDAM operation (no superclasses): + - Classification + - Phylogenetic tree visualisation + - Phylogenetic inference (from molecular sequences) + EDAM topic: + - Phylogeny + - Evolutionary biology + - Cladistics + - Genotype and phenotype + - Phylogenomics + EDAM topic (no superclasses): + - Cladistics + - Genotype and phenotype + - Phylogenomics + Galaxy tool ids: + - usher_matutils + - usher + Galaxy wrapper id: usher + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher + Galaxy wrapper version: 0.2.1 + No. of tool users (5 years) (usegalaxy.eu): 1060 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1060 + No. of tool users (all time) (usegalaxy.eu): 1060 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1060 + Source: https://github.com/yatisht/usher + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Phylogenetics + ToolShed id: usher + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + biii: null + bio.tool description: The UShER toolkit includes a set of tools for for rapid, accurate + placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 + phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic + contact tracing in that its placement is orders of magnitude faster and more memory-efficient + than previous methods. + bio.tool id: usher + bio.tool ids: + - usher + bio.tool name: usher +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: valet + Conda version: '1.0' + Date of first commit of the suite: '2017-11-16' + Description: A pipeline for detecting mis-assemblies in metagenomic assemblies. + EDAM operation: + - Sequence assembly + - Sequence assembly visualisation + EDAM operation (no superclasses): + - Sequence assembly + - Sequence assembly visualisation + EDAM topic: + - Metagenomics + - Sequence assembly + EDAM topic (no superclasses): + - Metagenomics + - Sequence assembly + Galaxy tool ids: + - valet + Galaxy wrapper id: valet + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 518 + No. of tool users (5 years) (usegalaxy.org): 234 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 752 + No. of tool users (all time) (usegalaxy.eu): 677 + No. of tool users (all time) (usegalaxy.org): 234 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 911 + Source: https://github.com/marbl/VALET + Status: To update + Tool usage (5 years) (usegalaxy.eu): 75 + Tool usage (5 years) (usegalaxy.org): 65 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 140 + Tool usage (all time) (usegalaxy.eu): 87 + Tool usage (all time) (usegalaxy.org): 65 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 152 + ToolShed categories: + - Metagenomics + ToolShed id: valet + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: VALET is a pipeline for detecting mis-assemblies in metagenomic + assemblies. + bio.tool id: valet + bio.tool ids: + - valet + bio.tool name: VALET +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: vapor + Conda version: 1.0.2 + Date of first commit of the suite: '2022-08-24' + Description: Classify Influenza samples from raw short read sequence data + EDAM operation: + - Data retrieval + - De-novo assembly + - Read mapping + EDAM operation (no superclasses): + - Data retrieval + - De-novo assembly + - Read mapping + EDAM topic: + - Whole genome sequencing + - Mapping + - Sequence assembly + EDAM topic (no superclasses): + - Whole genome sequencing + - Mapping + - Sequence assembly + Galaxy tool ids: + - vapor + Galaxy wrapper id: vapor + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 5936 + No. of tool users (5 years) (usegalaxy.org): 523 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6459 + No. of tool users (all time) (usegalaxy.eu): 5936 + No. of tool users (all time) (usegalaxy.org): 523 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6459 + Source: https://github.com/connor-lab/vapor + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 147 + Tool usage (5 years) (usegalaxy.org): 15 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 162 + Tool usage (all time) (usegalaxy.eu): 147 + Tool usage (all time) (usegalaxy.org): 15 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 162 + ToolShed categories: + - Sequence Analysis + ToolShed id: vapor + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: VAPOR is a tool for classification of Influenza samples from + raw short read sequence data for downstream bioinformatics analysis. VAPOR is + provided with a fasta file of full-length sequences (> 20,000) for a given segment, + a set of reads, and attempts to retrieve a reference that is closest to the sample + strain. + bio.tool id: vapor + bio.tool ids: + - vapor + bio.tool name: VAPOR +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2020-08-23' + Description: VarDict - calls SNVs and indels for tumour-normal pairs + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vardict_java + Galaxy wrapper id: vardict + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict + Galaxy wrapper version: 1.8.3 + No. of tool users (5 years) (usegalaxy.eu): 381 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 381 + No. of tool users (all time) (usegalaxy.eu): 381 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 381 + Source: https://github.com/AstraZeneca-NGS/VarDictJava + Status: To update + Tool usage (5 years) (usegalaxy.eu): 37 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 37 + Tool usage (all time) (usegalaxy.eu): 37 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 37 + ToolShed categories: + - Variant Analysis + ToolShed id: vardict_java + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 1 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 0 + Conda id: matplotlib + Conda version: null + Date of first commit of the suite: '2019-11-20' + Description: Collection of tools for analyzing variants in duplex consensus sequencing + (DCS) data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mut2read + - mut2sscs + - read2mut + Galaxy wrapper id: variant_analyzer + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer + Galaxy wrapper version: 2.0.0 + No. of tool users (5 years) (usegalaxy.eu): 95 + No. of tool users (5 years) (usegalaxy.org): 516 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 611 + No. of tool users (all time) (usegalaxy.eu): 95 + No. of tool users (all time) (usegalaxy.org): 516 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 611 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 14 + Tool usage (5 years) (usegalaxy.org): 67 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 81 + Tool usage (all time) (usegalaxy.eu): 14 + Tool usage (all time) (usegalaxy.org): 67 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 81 + ToolShed categories: + - Variant Analysis + ToolShed id: variant_analyzer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 3 + Conda id: varscan + Conda version: 2.4.6 + Date of first commit of the suite: '2018-11-29' + Description: VarScan is a variant caller for high-throughput sequencing data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - varscan_copynumber + - varscan_mpileup + - varscan_somatic + Galaxy wrapper id: varscan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan + Galaxy wrapper source: https://github.com/galaxyproject/iuc/tree/master/tools/varscan + Galaxy wrapper version: 2.4.3 + No. of tool users (5 years) (usegalaxy.eu): 10711 + No. of tool users (5 years) (usegalaxy.org): 16705 + No. of tool users (5 years) (usegalaxy.org.au): 1036 + No. of tool users (5 years) - all main servers: 28452 + No. of tool users (all time) (usegalaxy.eu): 11502 + No. of tool users (all time) (usegalaxy.org): 16705 + No. of tool users (all time) (usegalaxy.org.au): 1036 + No. of tool users (all time) - all main servers: 29243 + Source: https://dkoboldt.github.io/varscan/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1442 + Tool usage (5 years) (usegalaxy.org): 3135 + Tool usage (5 years) (usegalaxy.org.au): 100 + Tool usage (5 years) - all main servers: 4677 + Tool usage (all time) (usegalaxy.eu): 1560 + Tool usage (all time) (usegalaxy.org): 3135 + Tool usage (all time) (usegalaxy.org.au): 100 + Tool usage (all time) - all main servers: 4795 + ToolShed categories: + - Variant Analysis + ToolShed id: varscan + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 1 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: varvamp + Conda version: 1.2.1 + Date of first commit of the suite: '2024-01-27' + Description: Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly + diverse viruses + EDAM operation: + - PCR primer design + EDAM operation (no superclasses): + - PCR primer design + EDAM topic: + - Virology + - Probes and primers + EDAM topic (no superclasses): + - Virology + - Probes and primers + Galaxy tool ids: + - varvamp + Galaxy wrapper id: varvamp + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp + Galaxy wrapper source: https://github.com/jonas-fuchs/varVAMP + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 273 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 273 + No. of tool users (all time) (usegalaxy.eu): 273 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 273 + Source: https://github.com/jonas-fuchs/varVAMP/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 12 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 12 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - Sequence Analysis + ToolShed id: varvamp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: variable VirusAMPlicons (varVAMP) is a tool to design primers + for highly diverse viruses. The input is an alignment of your viral (full-genome) + sequences. + bio.tool id: varvamp + bio.tool ids: + - varvamp + bio.tool name: varVAMP +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: vcf2maf + Conda version: 1.6.22 + Date of first commit of the suite: '2022-06-28' + Description: 'vcf2maf: Convert VCF into MAF' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcf2maf + Galaxy wrapper id: vcf2maf + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf + Galaxy wrapper version: 1.6.21 + No. of tool users (5 years) (usegalaxy.eu): 1097 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 65 + No. of tool users (5 years) - all main servers: 1162 + No. of tool users (all time) (usegalaxy.eu): 1097 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 65 + No. of tool users (all time) - all main servers: 1162 + Source: https://github.com/mskcc/vcf2maf + Status: To update + Tool usage (5 years) (usegalaxy.eu): 46 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 5 + Tool usage (5 years) - all main servers: 51 + Tool usage (all time) (usegalaxy.eu): 46 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 5 + Tool usage (all time) - all main servers: 51 + ToolShed categories: + - Convert Formats + ToolShed id: vcf2maf + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: vcfanno + Conda version: 0.3.5 + Date of first commit of the suite: '2021-01-17' + Description: Annotate VCF files + EDAM operation: + - SNP annotation + EDAM operation (no superclasses): + - SNP annotation + EDAM topic: + - Genetic variation + - Data submission, annotation and curation + EDAM topic (no superclasses): + - Genetic variation + - Data submission, annotation and curation + Galaxy tool ids: + - vcfanno + Galaxy wrapper id: vcfanno + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/vcfanno/ + Galaxy wrapper version: 0.3.5 + No. of tool users (5 years) (usegalaxy.eu): 1139 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1139 + No. of tool users (all time) (usegalaxy.eu): 1139 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1139 + Source: https://github.com/brentp/vcfanno + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 174 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 174 + Tool usage (all time) (usegalaxy.eu): 174 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 174 + ToolShed categories: + - Variant Analysis + ToolShed id: vcfanno + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: Fast, flexible annotation of genetic variants. + bio.tool id: vcfanno + bio.tool ids: + - vcfanno + bio.tool name: vcfanno +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 0 + Conda id: r-vegan + Conda version: '2.3_4' + Date of first commit of the suite: '2015-08-27' + Description: an R package fo community ecologist + EDAM operation: + - Standardisation and normalisation + - Analysis + EDAM operation (no superclasses): + - Standardisation and normalisation + - Analysis + EDAM topic: + - Ecology + - Phylogenetics + - Environmental science + EDAM topic (no superclasses): + - Ecology + - Phylogenetics + - Environmental science + Galaxy tool ids: + - vegan_diversity + - vegan_fisher_alpha + - vegan_rarefaction + Galaxy wrapper id: vegan + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ + Galaxy wrapper version: 2.4-3 + No. of tool users (5 years) (usegalaxy.eu): 2157 + No. of tool users (5 years) (usegalaxy.org): 3930 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6087 + No. of tool users (all time) (usegalaxy.eu): 2287 + No. of tool users (all time) (usegalaxy.org): 5591 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7878 + Source: https://cran.r-project.org/package=vegan + Status: To update + Tool usage (5 years) (usegalaxy.eu): 198 + Tool usage (5 years) (usegalaxy.org): 446 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 644 + Tool usage (all time) (usegalaxy.eu): 209 + Tool usage (all time) (usegalaxy.org): 744 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 953 + ToolShed categories: + - Metagenomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 3 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + UseGalaxy.no: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: Ordination methods, diversity analysis and other functions + for community and vegetation ecologists + bio.tool id: vegan + bio.tool ids: + - vegan + bio.tool name: vegan +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: velocyto.py + Conda version: 0.17.17 + Date of first commit of the suite: '2021-04-30' + Description: Velocyto is a library for the analysis of RNA velocity. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - velocyto_cli + Galaxy wrapper id: velocyto + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto + Galaxy wrapper version: 0.17.17 + No. of tool users (5 years) (usegalaxy.eu): 7 + No. of tool users (5 years) (usegalaxy.org): 22 + No. of tool users (5 years) (usegalaxy.org.au): 16 + No. of tool users (5 years) - all main servers: 45 + No. of tool users (all time) (usegalaxy.eu): 7 + No. of tool users (all time) (usegalaxy.org): 22 + No. of tool users (all time) (usegalaxy.org.au): 16 + No. of tool users (all time) - all main servers: 45 + Source: http://velocyto.org/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 6 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 6 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Transcriptomics + - Single Cell + ToolShed id: velocyto + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: velvet + Conda version: 1.2.10 + Date of first commit of the suite: '2020-06-09' + Description: de novo genomic assembler specially designed for short read sequencing + technologies + EDAM operation: + - Formatting + - De-novo assembly + EDAM operation (no superclasses): + - Formatting + - De-novo assembly + EDAM topic: + - Sequence assembly + EDAM topic (no superclasses): + - Sequence assembly + Galaxy tool ids: + - velvetg + - velveth + Galaxy wrapper id: velvet + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 25171 + No. of tool users (5 years) (usegalaxy.org): 51187 + No. of tool users (5 years) (usegalaxy.org.au): 28546 + No. of tool users (5 years) - all main servers: 104904 + No. of tool users (all time) (usegalaxy.eu): 27943 + No. of tool users (all time) (usegalaxy.org): 51187 + No. of tool users (all time) (usegalaxy.org.au): 28619 + No. of tool users (all time) - all main servers: 107749 + Source: https://www.ebi.ac.uk/~zerbino/velvet/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3899 + Tool usage (5 years) (usegalaxy.org): 7557 + Tool usage (5 years) (usegalaxy.org.au): 3585 + Tool usage (5 years) - all main servers: 15041 + Tool usage (all time) (usegalaxy.eu): 4270 + Tool usage (all time) (usegalaxy.org): 7557 + Tool usage (all time) (usegalaxy.org.au): 3613 + Tool usage (all time) - all main servers: 15440 + ToolShed categories: + - Assembly + ToolShed id: velvet + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 2 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 2 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 2 + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: A de novo genomic assembler specially designed for short read + sequencing technologies, such as Solexa or 454 or SOLiD. + bio.tool id: velvet + bio.tool ids: + - velvet + bio.tool name: Velvet +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: velvet + Conda version: 1.2.10 + Date of first commit of the suite: '2017-12-19' + Description: Automatically optimize Velvet assemblies + EDAM operation: + - Optimisation and refinement + - Sequence assembly + EDAM operation (no superclasses): + - Optimisation and refinement + - Sequence assembly + EDAM topic: + - Genomics + - Sequence assembly + EDAM topic (no superclasses): + - Genomics + - Sequence assembly + Galaxy tool ids: + - velvetoptimiser + Galaxy wrapper id: velvet_optimiser + Galaxy wrapper owner: simon-gladman + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser + Galaxy wrapper version: 2.2.6+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 4715 + No. of tool users (5 years) (usegalaxy.org): 9575 + No. of tool users (5 years) (usegalaxy.org.au): 3271 + No. of tool users (5 years) - all main servers: 17561 + No. of tool users (all time) (usegalaxy.eu): 5343 + No. of tool users (all time) (usegalaxy.org): 9576 + No. of tool users (all time) (usegalaxy.org.au): 5524 + No. of tool users (all time) - all main servers: 20443 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 888 + Tool usage (5 years) (usegalaxy.org): 2117 + Tool usage (5 years) (usegalaxy.org.au): 1050 + Tool usage (5 years) - all main servers: 4055 + Tool usage (all time) (usegalaxy.eu): 965 + Tool usage (all time) (usegalaxy.org): 2117 + Tool usage (all time) (usegalaxy.org.au): 1397 + Tool usage (all time) - all main servers: 4479 + ToolShed categories: + - Assembly + ToolShed id: velvetoptimiser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This tool is designed to run as a wrapper script for the Velvet + assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. + bio.tool id: velvetoptimiser + bio.tool ids: + - velvetoptimiser + bio.tool name: VelvetOptimiser +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: verkko + Conda version: 2.2.1 + Date of first commit of the suite: '2023-01-24' + Description: Telomere-to-telomere assembly pipeline + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - verkko + Galaxy wrapper id: verkko + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko + Galaxy wrapper version: 1.3.1 + No. of tool users (5 years) (usegalaxy.eu): 48 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 48 + No. of tool users (all time) (usegalaxy.eu): 48 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 48 + Source: https://github.com/marbl/verkko + Status: To update + Tool usage (5 years) (usegalaxy.eu): 25 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 25 + Tool usage (all time) (usegalaxy.eu): 25 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 25 + ToolShed categories: + - Assembly + ToolShed id: verkko + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: vg + Conda version: 1.59.0 + Date of first commit of the suite: '2020-04-08' + Description: Variation graph data structures, interchange formats, alignment, genotyping, + and variant calling methods + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vg_convert + - vg_deconstruct + - vg_view + Galaxy wrapper id: vg + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg + Galaxy wrapper version: 1.23.0 + No. of tool users (5 years) (usegalaxy.eu): 478 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 478 + No. of tool users (all time) (usegalaxy.eu): 478 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 478 + Source: https://github.com/vgteam/vg + Status: To update + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 17 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 17 + ToolShed categories: + - Sequence Analysis + - Variant Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 3 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 3 + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + UseGalaxy.no: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: biopython + Conda version: '1.70' + Date of first commit of the suite: '2024-03-04' + Description: virAnnot wrappers + EDAM operation: + - Sequence annotation + - Sequence clustering + - Sequence cluster visualisation + EDAM operation (no superclasses): + - Sequence annotation + - Sequence clustering + - Sequence cluster visualisation + EDAM topic: + - Metagenomics + - Virology + - Microbial ecology + EDAM topic (no superclasses): + - Metagenomics + - Virology + - Microbial ecology + Galaxy tool ids: + - virannot_blast2tsv + - virannot_otu + - virAnnot_rps2tsv + Galaxy wrapper id: virAnnot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot + Galaxy wrapper version: 1.1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 94 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 94 + No. of tool users (all time) (usegalaxy.eu): 94 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 94 + Source: https://github.com/marieBvr/virAnnot + Status: To update + Tool usage (5 years) (usegalaxy.eu): 16 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 16 + Tool usage (all time) (usegalaxy.eu): 16 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 16 + ToolShed categories: + - Metagenomics + ToolShed id: virannot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + biii: null + bio.tool description: VirAnnot was build to ease the assembly, blast search, taxonomic + annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie + team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco + project "Plant Health Bioinformatics Network". See more.It is designed to identify + viruses in plant metagenomic data but it can be used to assemble and annotate + any sequences with the NCBI taxonomy. + bio.tool id: virannot + bio.tool ids: + - virannot + bio.tool name: virAnnot +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: virheat + Conda version: 0.7.1 + Date of first commit of the suite: '2024-05-15' + Description: generates a heatmap of allele frequencies from vcf files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - virheat + Galaxy wrapper id: virheat + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat + Galaxy wrapper version: 0.7.1 + No. of tool users (5 years) (usegalaxy.eu): 12 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 12 + No. of tool users (all time) (usegalaxy.eu): 12 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 12 + Source: https://github.com/jonas-fuchs/virHEAT + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Visualization + - Variant Analysis + ToolShed id: virheat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: VirHEAT tool generates multi-sample variant-frequency plots + from SnpEff-annotated viral variant lists. The tool provides a condensed look + at variant frequencies after mapping raw reads to a viral/bacterial reference + genome and compares multiple vcf files at the same time. + bio.tool id: virheat + bio.tool ids: + - virheat + bio.tool name: virHEAT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: numpy + Conda version: null + Date of first commit of the suite: '2022-09-13' + Description: Deep Learning method for novel virus detection in sequencing data + EDAM operation: + - Sequence classification + EDAM operation (no superclasses): + - Sequence classification + EDAM topic: + - Virology + EDAM topic (no superclasses): + - Virology + Galaxy tool ids: + - virhunter + Galaxy wrapper id: virhunter + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 574 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 574 + No. of tool users (all time) (usegalaxy.eu): 574 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 574 + Source: https://github.com/cbib/virhunter + Status: To update + Tool usage (5 years) (usegalaxy.eu): 76 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 76 + Tool usage (all time) (usegalaxy.eu): 76 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 76 + ToolShed categories: + - Machine Learning + ToolShed id: virhunter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: VirHunter is a deep learning method that uses Convolutional + Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing + datasets. More precisely, VirHunter classifies previously assembled contigs as + viral, host, and bacterial (contamination). + bio.tool id: virhunter + bio.tool ids: + - virhunter + bio.tool name: VirHunter +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-ggplot2 + Conda version: 2.2.1 + Date of first commit of the suite: '2018-10-14' + Description: Tool to create a Volcano Plot + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - volcanoplot + Galaxy wrapper id: volcanoplot + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot + Galaxy wrapper version: 0.0.6 + No. of tool users (5 years) (usegalaxy.eu): 34917 + No. of tool users (5 years) (usegalaxy.org): 54931 + No. of tool users (5 years) (usegalaxy.org.au): 7183 + No. of tool users (5 years) - all main servers: 97031 + No. of tool users (all time) (usegalaxy.eu): 36852 + No. of tool users (all time) (usegalaxy.org): 54931 + No. of tool users (all time) (usegalaxy.org.au): 7183 + No. of tool users (all time) - all main servers: 98966 + Source: https://ggplot2.tidyverse.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3670 + Tool usage (5 years) (usegalaxy.org): 5597 + Tool usage (5 years) (usegalaxy.org.au): 905 + Tool usage (5 years) - all main servers: 10172 + Tool usage (all time) (usegalaxy.eu): 3786 + Tool usage (all time) (usegalaxy.org): 5597 + Tool usage (all time) (usegalaxy.org.au): 905 + Tool usage (all time) - all main servers: 10288 + ToolShed categories: + - Visualization + - Transcriptomics + - Statistics + ToolShed id: volcanoplot + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 8 + Available on UseGalaxy.fr: 8 + Available on UseGalaxy.org (Main): 8 + Available on UseGalaxy.org.au: 8 + Conda id: vsearch + Conda version: 2.29.0 + Date of first commit of the suite: '2015-07-01' + Description: VSEARCH including searching, clustering, chimera detection, dereplication, + sorting, masking and shuffling of sequences. + EDAM operation: + - DNA mapping + - Chimera detection + EDAM operation (no superclasses): + - DNA mapping + - Chimera detection + EDAM topic: + - Metagenomics + - Sequence analysis + EDAM topic (no superclasses): + - Metagenomics + - Sequence analysis + Galaxy tool ids: + - vsearch_alignment + - vsearch_chimera_detection + - vsearch_clustering + - vsearch_dereplication + - vsearch_masking + - vsearch_search + - vsearch_shuffling + - vsearch_sorting + Galaxy wrapper id: vsearch + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch + Galaxy wrapper version: 2.8.3 + No. of tool users (5 years) (usegalaxy.eu): 9694 + No. of tool users (5 years) (usegalaxy.org): 12282 + No. of tool users (5 years) (usegalaxy.org.au): 5334 + No. of tool users (5 years) - all main servers: 27310 + No. of tool users (all time) (usegalaxy.eu): 10338 + No. of tool users (all time) (usegalaxy.org): 53546 + No. of tool users (all time) (usegalaxy.org.au): 5672 + No. of tool users (all time) - all main servers: 69556 + Source: https://github.com/torognes/vsearch + Status: To update + Tool usage (5 years) (usegalaxy.eu): 559 + Tool usage (5 years) (usegalaxy.org): 1031 + Tool usage (5 years) (usegalaxy.org.au): 246 + Tool usage (5 years) - all main servers: 1836 + Tool usage (all time) (usegalaxy.eu): 628 + Tool usage (all time) (usegalaxy.org): 2007 + Tool usage (all time) (usegalaxy.org.au): 277 + Tool usage (all time) - all main servers: 2912 + ToolShed categories: + - Sequence Analysis + ToolShed id: vsearch + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 8 + Tools available on GalaxyTrakr: 8 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 8 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 8 + Tools available on UseGalaxy.cz: 8 + Tools available on UseGalaxy.eu: 8 + Tools available on UseGalaxy.fr: 8 + Tools available on UseGalaxy.no: 8 + Tools available on UseGalaxy.org (Main): 8 + Tools available on UseGalaxy.org.au: 8 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 8 + UseGalaxy.cz: 8 + UseGalaxy.eu: 8 + UseGalaxy.fr: 8 + UseGalaxy.no: 8 + UseGalaxy.or: 8 + biii: null + bio.tool description: High-throughput search and clustering sequence analysis tool. + It supports de novo and reference based chimera detection, clustering, full-length + and prefix dereplication, reverse complementation, masking, all-vs-all pairwise + global alignment, exact and global alignment searching, shuffling, subsampling + and sorting. It also supports FASTQ file analysis, filtering and conversion. + bio.tool id: vsearch + bio.tool ids: + - vsearch + bio.tool name: VSEARCH +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pysam + Conda version: 0.22.1 + Date of first commit of the suite: '2020-04-27' + Description: The vSNP tools are critical components of several workflows that validate + SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vsnp_add_zero_coverage + - vsnp_build_tables + - vsnp_determine_ref_from_data + - vsnp_get_snps + - vsnp_statistics + Galaxy wrapper id: vsnp + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp + Galaxy wrapper version: 3.0.6 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/USDA-VS/vSNP + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: vsnp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: curl + Conda version: null + Date of first commit of the suite: '2016-07-19' + Description: provides simple weather in text format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - simple_weather + Galaxy wrapper id: weather_app + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app + Galaxy wrapper version: 0.1.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://wttr.in/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Visualization + - Web Services + ToolShed id: simpleweather + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: weblogo + Conda version: 3.7.9 + Date of first commit of the suite: '2017-11-17' + Description: Sequence Logo generator for fasta + EDAM operation: + - Sequence cluster visualisation + - Sequence visualisation + - Sequence motif recognition + EDAM operation (no superclasses): + - Sequence cluster visualisation + - Sequence visualisation + - Sequence motif recognition + EDAM topic: + - Nucleic acid sites, features and motifs + - Sequence analysis + EDAM topic (no superclasses): + - Nucleic acid sites, features and motifs + - Sequence analysis + Galaxy tool ids: + - rgweblogo3 + Galaxy wrapper id: weblogo3 + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 + Galaxy wrapper version: 3.5.0 + No. of tool users (5 years) (usegalaxy.eu): 2720 + No. of tool users (5 years) (usegalaxy.org): 10299 + No. of tool users (5 years) (usegalaxy.org.au): 1226 + No. of tool users (5 years) - all main servers: 14245 + No. of tool users (all time) (usegalaxy.eu): 2818 + No. of tool users (all time) (usegalaxy.org): 30578 + No. of tool users (all time) (usegalaxy.org.au): 1285 + No. of tool users (all time) - all main servers: 34681 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 206 + Tool usage (5 years) (usegalaxy.org): 1354 + Tool usage (5 years) (usegalaxy.org.au): 50 + Tool usage (5 years) - all main servers: 1610 + Tool usage (all time) (usegalaxy.eu): 228 + Tool usage (all time) (usegalaxy.org): 3657 + Tool usage (all time) (usegalaxy.org.au): 59 + Tool usage (all time) - all main servers: 3944 + ToolShed categories: + - Graphics + ToolShed id: weblogo3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Web-based application designed to make generate sequence logos. + bio.tool id: weblogo + bio.tool ids: + - weblogo + bio.tool name: WebLogo +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: blast + Conda version: 2.16.0 + Date of first commit of the suite: '2023-12-14' + Description: Identify repetitive regions using WindowMasker + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - windowmasker_mkcounts + - windowmasker_ustat + Galaxy wrapper id: windowmasker + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 537 + No. of tool users (5 years) (usegalaxy.org): 12 + No. of tool users (5 years) (usegalaxy.org.au): 297 + No. of tool users (5 years) - all main servers: 846 + No. of tool users (all time) (usegalaxy.eu): 537 + No. of tool users (all time) (usegalaxy.org): 12 + No. of tool users (all time) (usegalaxy.org.au): 297 + No. of tool users (all time) - all main servers: 846 + Source: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 19 + Tool usage (5 years) (usegalaxy.org): 7 + Tool usage (5 years) (usegalaxy.org.au): 2 + Tool usage (5 years) - all main servers: 28 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 7 + Tool usage (all time) (usegalaxy.org.au): 2 + Tool usage (all time) - all main servers: 28 + ToolShed categories: + - Sequence Analysis + ToolShed id: windowmasker + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: winnowmap + Conda version: '2.03' + Date of first commit of the suite: '2021-04-29' + Description: A long-read mapping tool optimized for mapping ONT and PacBio reads + to repetitive reference sequences. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - winnowmap + Galaxy wrapper id: winnowmap + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap + Galaxy wrapper version: '2.03' + No. of tool users (5 years) (usegalaxy.eu): 279 + No. of tool users (5 years) (usegalaxy.org): 12 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 291 + No. of tool users (all time) (usegalaxy.eu): 279 + No. of tool users (all time) (usegalaxy.org): 12 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 291 + Source: https://github.com/marbl/Winnowmap + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 46 + Tool usage (5 years) (usegalaxy.org): 4 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 50 + Tool usage (all time) (usegalaxy.eu): 46 + Tool usage (all time) (usegalaxy.org): 4 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 50 + ToolShed categories: + - Next Gen Mappers + ToolShed id: winnowmap + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: perl-xml-xpath + Conda version: '1.47' + Date of first commit of the suite: '2015-04-14' + Description: XPath XML querying tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - xpath + Galaxy wrapper id: xpath + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 128 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 128 + No. of tool users (all time) (usegalaxy.eu): 235 + No. of tool users (all time) (usegalaxy.org): 1 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 236 + Source: http://search.cpan.org/dist/XML-XPath/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Text Manipulation + ToolShed id: xpath + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: yahs + Conda version: 1.2.2 + Date of first commit of the suite: '2022-06-28' + Description: Yet Another Hi-C scaffolding tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - yahs + Galaxy wrapper id: yahs + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs + Galaxy wrapper version: 1.2a.2 + No. of tool users (5 years) (usegalaxy.eu): 618 + No. of tool users (5 years) (usegalaxy.org): 336 + No. of tool users (5 years) (usegalaxy.org.au): 588 + No. of tool users (5 years) - all main servers: 1542 + No. of tool users (all time) (usegalaxy.eu): 618 + No. of tool users (all time) (usegalaxy.org): 336 + No. of tool users (all time) (usegalaxy.org.au): 588 + No. of tool users (all time) - all main servers: 1542 + Source: https://github.com/c-zhou/yahs + Status: To update + Tool usage (5 years) (usegalaxy.eu): 176 + Tool usage (5 years) (usegalaxy.org): 62 + Tool usage (5 years) (usegalaxy.org.au): 25 + Tool usage (5 years) - all main servers: 263 + Tool usage (all time) (usegalaxy.eu): 176 + Tool usage (all time) (usegalaxy.org): 62 + Tool usage (all time) (usegalaxy.org.au): 25 + Tool usage (all time) - all main servers: 263 + ToolShed categories: + - Assembly + ToolShed id: yahs + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: zerone + Conda version: '1.0' + Date of first commit of the suite: '2018-09-05' + Description: ChIP-seq discretization and quality control + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - zerone + Galaxy wrapper id: zerone + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 83 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 83 + No. of tool users (all time) (usegalaxy.eu): 96 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 96 + Source: https://github.com/nanakiksc/zerone + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - ChIP-seq + ToolShed id: zerone + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bamtools + Conda version: 2.5.2 + Date of first commit of the suite: '2017-06-09' + Description: Operate on and transform BAM datasets in various ways using bamtools + EDAM operation: + - Data handling + - Sequence alignment analysis + EDAM operation (no superclasses): + - Data handling + - Sequence alignment analysis + EDAM topic: + - Sequencing + - Data management + - Sequence analysis + EDAM topic (no superclasses): + - Sequencing + - Sequence analysis + Galaxy tool ids: + - bamtools + Galaxy wrapper id: bamtools + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools + Galaxy wrapper version: 2.5.2 + No. of tool users (5 years) (usegalaxy.eu): 14693 + No. of tool users (5 years) (usegalaxy.org): 61872 + No. of tool users (5 years) (usegalaxy.org.au): 39 + No. of tool users (5 years) - all main servers: 76604 + No. of tool users (all time) (usegalaxy.eu): 15620 + No. of tool users (all time) (usegalaxy.org): 101400 + No. of tool users (all time) (usegalaxy.org.au): 39 + No. of tool users (all time) - all main servers: 117059 + Source: https://github.com/pezmaster31/bamtools + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 653 + Tool usage (5 years) (usegalaxy.org): 1656 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 2312 + Tool usage (all time) (usegalaxy.eu): 721 + Tool usage (all time) (usegalaxy.org): 5678 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 6402 + ToolShed categories: + - Sequence Analysis + - SAM + ToolShed id: bamtools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: BamTools provides a fast, flexible C++ API & toolkit for reading, + writing, and managing BAM files. + bio.tool id: bamtools + bio.tool ids: + - bamtools + bio.tool name: BamTools +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bamtools + Conda version: 2.5.2 + Date of first commit of the suite: '2017-06-09' + Description: Filter BAM datasets on various attributes using bamtools filter + EDAM operation: + - Data handling + - Sequence alignment analysis + EDAM operation (no superclasses): + - Data handling + - Sequence alignment analysis + EDAM topic: + - Sequencing + - Data management + - Sequence analysis + EDAM topic (no superclasses): + - Sequencing + - Sequence analysis + Galaxy tool ids: + - bamFilter + Galaxy wrapper id: bamtools_filter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter + Galaxy wrapper version: 2.5.2 + No. of tool users (5 years) (usegalaxy.eu): 115954 + No. of tool users (5 years) (usegalaxy.org): 95433 + No. of tool users (5 years) (usegalaxy.org.au): 5793 + No. of tool users (5 years) - all main servers: 217180 + No. of tool users (all time) (usegalaxy.eu): 124795 + No. of tool users (all time) (usegalaxy.org): 142254 + No. of tool users (all time) (usegalaxy.org.au): 5793 + No. of tool users (all time) - all main servers: 272842 + Source: https://github.com/pezmaster31/bamtools + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2994 + Tool usage (5 years) (usegalaxy.org): 6712 + Tool usage (5 years) (usegalaxy.org.au): 497 + Tool usage (5 years) - all main servers: 10203 + Tool usage (all time) (usegalaxy.eu): 3180 + Tool usage (all time) (usegalaxy.org): 10660 + Tool usage (all time) (usegalaxy.org.au): 497 + Tool usage (all time) - all main servers: 14337 + ToolShed categories: + - Sequence Analysis + - SAM + ToolShed id: bamtools_filter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: BamTools provides a fast, flexible C++ API & toolkit for reading, + writing, and managing BAM files. + bio.tool id: bamtools + bio.tool ids: + - bamtools + bio.tool name: BamTools +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 3 + Conda id: bamtools + Conda version: 2.5.2 + Date of first commit of the suite: '2017-06-09' + Description: Utility for filtering BAM files. It is based on the BAMtools suiteof + tools by Derek Barnett. + EDAM operation: + - Data handling + - Sequence alignment analysis + EDAM operation (no superclasses): + - Data handling + - Sequence alignment analysis + EDAM topic: + - Sequencing + - Data management + - Sequence analysis + EDAM topic (no superclasses): + - Sequencing + - Sequence analysis + Galaxy tool ids: + - bamtools_split_mapped + - bamtools_split_paired + - bamtools_split_ref + - bamtools_split_tag + Galaxy wrapper id: bamtools_split + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split + Galaxy wrapper version: 2.5.2 + No. of tool users (5 years) (usegalaxy.eu): 9073 + No. of tool users (5 years) (usegalaxy.org): 2746 + No. of tool users (5 years) (usegalaxy.org.au): 103 + No. of tool users (5 years) - all main servers: 11922 + No. of tool users (all time) (usegalaxy.eu): 9073 + No. of tool users (all time) (usegalaxy.org): 2746 + No. of tool users (all time) (usegalaxy.org.au): 103 + No. of tool users (all time) - all main servers: 11922 + Source: https://github.com/pezmaster31/bamtools + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 401 + Tool usage (5 years) (usegalaxy.org): 224 + Tool usage (5 years) (usegalaxy.org.au): 10 + Tool usage (5 years) - all main servers: 635 + Tool usage (all time) (usegalaxy.eu): 401 + Tool usage (all time) (usegalaxy.org): 224 + Tool usage (all time) (usegalaxy.org.au): 10 + Tool usage (all time) - all main servers: 635 + ToolShed categories: + - Sequence Analysis + - SAM + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 1 + UseGalaxy.or: 3 + biii: null + bio.tool description: BamTools provides a fast, flexible C++ API & toolkit for reading, + writing, and managing BAM files. + bio.tool id: bamtools + bio.tool ids: + - bamtools + bio.tool name: BamTools +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 3 + Available on UseGalaxy.org.au: 0 + Conda id: biotradis + Conda version: 1.4.5 + Date of first commit of the suite: '2020-01-17' + Description: Bio-Tradis is a tool suite dedicated to essentiality analyses with + TraDis data. + EDAM operation: + - Sequence analysis + EDAM operation (no superclasses): + - Sequence analysis + EDAM topic: + - Mobile genetic elements + - Workflows + EDAM topic (no superclasses): + - Mobile genetic elements + - Workflows + Galaxy tool ids: + - bacteria_tradis + - tradis_essentiality + - tradis_gene_insert_sites + Galaxy wrapper id: biotradis + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis + Galaxy wrapper version: 1.4.5 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 6243 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6243 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 6243 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6243 + Source: https://www.sanger.ac.uk/science/tools/bio-tradis + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 375 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 375 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 375 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 375 + ToolShed categories: + - Genome annotation + ToolShed id: biotradis + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 3 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.or: 3 + biii: null + bio.tool description: The Bio::TraDIS pipeline provides software utilities for the + processing, mapping, and analysis of transposon insertion sequencing data. The + pipeline was designed with the data from the TraDIS sequencing protocol in mind, + but should work with a variety of transposon insertion sequencing protocols as + long as they produce data in the expected format. + bio.tool id: biotradis + bio.tool ids: + - biotradis + bio.tool name: biotradis +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: cufflinks + Conda version: 2.2.1 + Date of first commit of the suite: '2020-06-08' + Description: Galaxy wrappers for the Cuffcompare tool. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cuffcompare + Galaxy wrapper id: cuffcompare + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 768 + No. of tool users (5 years) (usegalaxy.org): 2205 + No. of tool users (5 years) (usegalaxy.org.au): 251 + No. of tool users (5 years) - all main servers: 3224 + No. of tool users (all time) (usegalaxy.eu): 1199 + No. of tool users (all time) (usegalaxy.org): 24981 + No. of tool users (all time) (usegalaxy.org.au): 493 + No. of tool users (all time) - all main servers: 26673 + Source: http://cole-trapnell-lab.github.io/cufflinks/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 171 + Tool usage (5 years) (usegalaxy.org): 754 + Tool usage (5 years) (usegalaxy.org.au): 46 + Tool usage (5 years) - all main servers: 971 + Tool usage (all time) (usegalaxy.eu): 300 + Tool usage (all time) (usegalaxy.org): 5750 + Tool usage (all time) (usegalaxy.org.au): 98 + Tool usage (all time) - all main servers: 6148 + ToolShed categories: + - Transcriptomics + ToolShed id: cuffcompare + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 1 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: cufflinks + Conda version: 2.2.1 + Date of first commit of the suite: '2020-06-08' + Description: Galaxy wrappers for the Cuffdiff tool. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cuffdiff + Galaxy wrapper id: cuffdiff + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 4176 + No. of tool users (5 years) (usegalaxy.org): 24284 + No. of tool users (5 years) (usegalaxy.org.au): 971 + No. of tool users (5 years) - all main servers: 29431 + No. of tool users (all time) (usegalaxy.eu): 6065 + No. of tool users (all time) (usegalaxy.org): 117007 + No. of tool users (all time) (usegalaxy.org.au): 4231 + No. of tool users (all time) - all main servers: 127303 + Source: http://cole-trapnell-lab.github.io/cufflinks/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 564 + Tool usage (5 years) (usegalaxy.org): 4952 + Tool usage (5 years) (usegalaxy.org.au): 193 + Tool usage (5 years) - all main servers: 5709 + Tool usage (all time) (usegalaxy.eu): 725 + Tool usage (all time) (usegalaxy.org): 20249 + Tool usage (all time) (usegalaxy.org.au): 616 + Tool usage (all time) - all main servers: 21590 + ToolShed categories: + - Transcriptomics + ToolShed id: cuffdiff + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 1 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: cufflinks + Conda version: 2.2.1 + Date of first commit of the suite: '2020-06-08' + Description: Galaxy wrappers for the Cufflinks tool. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cufflinks + Galaxy wrapper id: cufflinks + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 26122 + No. of tool users (5 years) (usegalaxy.org): 70653 + No. of tool users (5 years) (usegalaxy.org.au): 3963 + No. of tool users (5 years) - all main servers: 100738 + No. of tool users (all time) (usegalaxy.eu): 33320 + No. of tool users (all time) (usegalaxy.org): 349091 + No. of tool users (all time) (usegalaxy.org.au): 10315 + No. of tool users (all time) - all main servers: 392726 + Source: http://cole-trapnell-lab.github.io/cufflinks/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 870 + Tool usage (5 years) (usegalaxy.org): 6984 + Tool usage (5 years) (usegalaxy.org.au): 440 + Tool usage (5 years) - all main servers: 8294 + Tool usage (all time) (usegalaxy.eu): 1213 + Tool usage (all time) (usegalaxy.org): 27076 + Tool usage (all time) (usegalaxy.org.au): 836 + Tool usage (all time) - all main servers: 29125 + ToolShed categories: + - Transcriptomics + ToolShed id: cufflinks + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 1 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: cufflinks + Conda version: 2.2.1 + Date of first commit of the suite: '2020-06-08' + Description: Galaxy wrappers for the Cuffmerge tool. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cuffmerge + Galaxy wrapper id: cuffmerge + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 2406 + No. of tool users (5 years) (usegalaxy.org): 20978 + No. of tool users (5 years) (usegalaxy.org.au): 1209 + No. of tool users (5 years) - all main servers: 24593 + No. of tool users (all time) (usegalaxy.eu): 3448 + No. of tool users (all time) (usegalaxy.org): 67769 + No. of tool users (all time) (usegalaxy.org.au): 3057 + No. of tool users (all time) - all main servers: 74274 + Source: http://cole-trapnell-lab.github.io/cufflinks/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 351 + Tool usage (5 years) (usegalaxy.org): 3641 + Tool usage (5 years) (usegalaxy.org.au): 227 + Tool usage (5 years) - all main servers: 4219 + Tool usage (all time) (usegalaxy.eu): 637 + Tool usage (all time) (usegalaxy.org): 13764 + Tool usage (all time) (usegalaxy.org.au): 573 + Tool usage (all time) - all main servers: 14974 + ToolShed categories: + - Transcriptomics + ToolShed id: cuffmerge + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 1 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: cufflinks + Conda version: 2.2.1 + Date of first commit of the suite: '2020-06-08' + Description: The Cuffnorm tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cuffnorm + Galaxy wrapper id: cuffnorm + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 374 + No. of tool users (5 years) (usegalaxy.org): 1032 + No. of tool users (5 years) (usegalaxy.org.au): 262 + No. of tool users (5 years) - all main servers: 1668 + No. of tool users (all time) (usegalaxy.eu): 701 + No. of tool users (all time) (usegalaxy.org): 13499 + No. of tool users (all time) (usegalaxy.org.au): 322 + No. of tool users (all time) - all main servers: 14522 + Source: http://cole-trapnell-lab.github.io/cufflinks/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 81 + Tool usage (5 years) (usegalaxy.org): 273 + Tool usage (5 years) (usegalaxy.org.au): 53 + Tool usage (5 years) - all main servers: 407 + Tool usage (all time) (usegalaxy.eu): 114 + Tool usage (all time) (usegalaxy.org): 1166 + Tool usage (all time) (usegalaxy.org.au): 70 + Tool usage (all time) - all main servers: 1350 + ToolShed categories: + - Transcriptomics + ToolShed id: cuffnorm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: cufflinks + Conda version: 2.2.1 + Date of first commit of the suite: '2020-06-08' + Description: The Cuffquant tool + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cuffquant + Galaxy wrapper id: cuffquant + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant + Galaxy wrapper version: 2.2.1 + No. of tool users (5 years) (usegalaxy.eu): 408 + No. of tool users (5 years) (usegalaxy.org): 1964 + No. of tool users (5 years) (usegalaxy.org.au): 308 + No. of tool users (5 years) - all main servers: 2680 + No. of tool users (all time) (usegalaxy.eu): 732 + No. of tool users (all time) (usegalaxy.org): 15883 + No. of tool users (all time) (usegalaxy.org.au): 422 + No. of tool users (all time) - all main servers: 17037 + Source: http://cole-trapnell-lab.github.io/cufflinks/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 54 + Tool usage (5 years) (usegalaxy.org): 267 + Tool usage (5 years) (usegalaxy.org.au): 26 + Tool usage (5 years) - all main servers: 347 + Tool usage (all time) (usegalaxy.eu): 71 + Tool usage (all time) (usegalaxy.org): 1310 + Tool usage (all time) (usegalaxy.org.au): 46 + Tool usage (all time) - all main servers: 1427 + ToolShed categories: + - Transcriptomics + ToolShed id: cuffquant + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2017-07-10' + Description: Length Distribution chart + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fasta_clipping_histogram + Galaxy wrapper id: fasta_clipping_histogram + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 5191 + No. of tool users (5 years) - all main servers: 5191 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 5367 + No. of tool users (all time) - all main servers: 5367 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 104 + Tool usage (5 years) - all main servers: 104 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 130 + Tool usage (all time) - all main servers: 130 + ToolShed categories: + - Fasta Manipulation + - Graphics + - Statistics + ToolShed id: fasta_clipping_histogram + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2018-04-24' + Description: FASTA Width formatter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fasta_formatter + Galaxy wrapper id: fasta_formatter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 5235 + No. of tool users (5 years) (usegalaxy.org): 4060 + No. of tool users (5 years) (usegalaxy.org.au): 816 + No. of tool users (5 years) - all main servers: 10111 + No. of tool users (all time) (usegalaxy.eu): 5486 + No. of tool users (all time) (usegalaxy.org): 25609 + No. of tool users (all time) (usegalaxy.org.au): 1093 + No. of tool users (all time) - all main servers: 32188 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 237 + Tool usage (5 years) (usegalaxy.org): 480 + Tool usage (5 years) (usegalaxy.org.au): 73 + Tool usage (5 years) - 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cshl_fasta_nucleotides_changer + Galaxy wrapper id: fasta_nucleotide_changer + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 497 + No. of tool users (5 years) (usegalaxy.org): 2249 + No. of tool users (5 years) (usegalaxy.org.au): 415 + No. of tool users (5 years) - all main servers: 3161 + No. of tool users (all time) (usegalaxy.eu): 808 + No. of tool users (all time) (usegalaxy.org): 5479 + No. of tool users (all time) (usegalaxy.org.au): 437 + No. of tool users (all time) - all main servers: 6724 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 71 + Tool usage (5 years) (usegalaxy.org): 216 + Tool usage (5 years) (usegalaxy.org.au): 18 + Tool usage (5 years) - 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cshl_fastq_quality_boxplot + Galaxy wrapper id: fastq_quality_boxplot + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 1271 + No. of tool users (5 years) (usegalaxy.org): 12763 + No. of tool users (5 years) (usegalaxy.org.au): 430 + No. of tool users (5 years) - all main servers: 14464 + No. of tool users (all time) (usegalaxy.eu): 1393 + No. of tool users (all time) (usegalaxy.org): 58819 + No. of tool users (all time) (usegalaxy.org.au): 479 + No. of tool users (all time) - all main servers: 60691 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 131 + Tool usage (5 years) (usegalaxy.org): 2073 + Tool usage (5 years) (usegalaxy.org.au): 32 + Tool usage (5 years) - 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cshl_fastq_quality_converter + Galaxy wrapper id: fastq_quality_converter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 335 + No. of tool users (5 years) (usegalaxy.org): 1583 + No. of tool users (5 years) (usegalaxy.org.au): 1131 + No. of tool users (5 years) - all main servers: 3049 + No. of tool users (all time) (usegalaxy.eu): 352 + No. of tool users (all time) (usegalaxy.org): 9696 + No. of tool users (all time) (usegalaxy.org.au): 1254 + No. of tool users (all time) - all main servers: 11302 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 44 + Tool usage (5 years) (usegalaxy.org): 269 + Tool usage (5 years) (usegalaxy.org.au): 15 + Tool usage (5 years) - 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cshl_fastq_quality_filter + Galaxy wrapper id: fastq_quality_filter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 17279 + No. of tool users (5 years) (usegalaxy.org): 55268 + No. of tool users (5 years) (usegalaxy.org.au): 7685 + No. of tool users (5 years) - all main servers: 80232 + No. of tool users (all time) (usegalaxy.eu): 18386 + No. of tool users (all time) (usegalaxy.org): 136888 + No. of tool users (all time) (usegalaxy.org.au): 9356 + No. of tool users (all time) - all main servers: 164630 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 3826 + Tool usage (5 years) (usegalaxy.org): 6055 + Tool usage (5 years) (usegalaxy.org.au): 1854 + Tool usage (5 years) - all main servers: 11735 + Tool usage (all time) (usegalaxy.eu): 4062 + Tool usage (all time) (usegalaxy.org): 12590 + Tool usage (all time) (usegalaxy.org.au): 2043 + Tool usage (all time) - all main servers: 18695 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastq_quality_filter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2016-09-17' + Description: FASTQ to FASTA converter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastq_to_fasta + Galaxy wrapper id: fastq_to_fasta + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 36069 + No. of tool users (5 years) (usegalaxy.org): 45213 + No. of tool users (5 years) (usegalaxy.org.au): 8457 + No. of tool users (5 years) - all main servers: 89739 + No. of tool users (all time) (usegalaxy.eu): 37805 + No. of tool users (all time) (usegalaxy.org): 99852 + No. of tool users (all time) (usegalaxy.org.au): 13335 + No. of tool users (all time) - all main servers: 150992 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1151 + Tool usage (5 years) (usegalaxy.org): 2691 + Tool usage (5 years) (usegalaxy.org.au): 408 + Tool usage (5 years) - all main servers: 4250 + Tool usage (all time) (usegalaxy.eu): 1234 + Tool usage (all time) (usegalaxy.org): 6370 + Tool usage (all time) (usegalaxy.org.au): 609 + Tool usage (all time) - all main servers: 8213 + ToolShed categories: + - Fasta Manipulation + - Convert Formats + ToolShed id: fastq_to_fasta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2017-07-10' + Description: Remove sequencing artifacts + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastx_artifacts_filter + Galaxy wrapper id: fastx_artifacts_filter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 1769 + No. of tool users (5 years) (usegalaxy.org): 6948 + No. of tool users (5 years) (usegalaxy.org.au): 623 + No. of tool users (5 years) - all main servers: 9340 + No. of tool users (all time) (usegalaxy.eu): 2020 + No. of tool users (all time) (usegalaxy.org): 24960 + No. of tool users (all time) (usegalaxy.org.au): 998 + No. of tool users (all time) - all main servers: 27978 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 88 + Tool usage (5 years) (usegalaxy.org): 358 + Tool usage (5 years) (usegalaxy.org.au): 32 + Tool usage (5 years) - 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cshl_fastx_barcode_splitter + Galaxy wrapper id: fastx_barcode_splitter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 16957 + No. of tool users (5 years) (usegalaxy.org): 37001 + No. of tool users (5 years) (usegalaxy.org.au): 863 + No. of tool users (5 years) - all main servers: 54821 + No. of tool users (all time) (usegalaxy.eu): 18124 + No. of tool users (all time) (usegalaxy.org): 89126 + No. of tool users (all time) (usegalaxy.org.au): 989 + No. of tool users (all time) - all main servers: 108239 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 225 + Tool usage (5 years) (usegalaxy.org): 919 + Tool usage (5 years) (usegalaxy.org.au): 56 + Tool usage (5 years) - all main servers: 1200 + Tool usage (all time) (usegalaxy.eu): 260 + Tool usage (all time) (usegalaxy.org): 2720 + Tool usage (all time) (usegalaxy.org.au): 68 + Tool usage (all time) - all main servers: 3048 + ToolShed categories: + - Fasta Manipulation + - Fastq Manipulation + ToolShed id: fastx_barcode_splitter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2017-07-10' + Description: Clip adapter sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastx_clipper + Galaxy wrapper id: fastx_clipper + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 3140 + No. of tool users (5 years) (usegalaxy.org): 13975 + No. of tool users (5 years) (usegalaxy.org.au): 409 + No. of tool users (5 years) - all main servers: 17524 + No. of tool users (all time) (usegalaxy.eu): 3520 + No. of tool users (all time) (usegalaxy.org): 117900 + No. of tool users (all time) (usegalaxy.org.au): 712 + No. of tool users (all time) - all main servers: 122132 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 178 + Tool usage (5 years) (usegalaxy.org): 1198 + Tool usage (5 years) (usegalaxy.org.au): 36 + Tool usage (5 years) - all main servers: 1412 + Tool usage (all time) (usegalaxy.eu): 212 + Tool usage (all time) (usegalaxy.org): 6006 + Tool usage (all time) (usegalaxy.org.au): 55 + Tool usage (all time) - all main servers: 6273 + ToolShed categories: + - Fasta Manipulation + - Fastq Manipulation + ToolShed id: fastx_clipper + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2017-07-10' + Description: Collapse sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastx_collapser + Galaxy wrapper id: fastx_collapser + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 64187 + No. of tool users (5 years) (usegalaxy.org): 87477 + No. of tool users (5 years) (usegalaxy.org.au): 16563 + No. of tool users (5 years) - all main servers: 168227 + No. of tool users (all time) (usegalaxy.eu): 67981 + No. of tool users (all time) (usegalaxy.org): 185555 + No. of tool users (all time) (usegalaxy.org.au): 17125 + No. of tool users (all time) - all main servers: 270661 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 326 + Tool usage (5 years) (usegalaxy.org): 781 + Tool usage (5 years) (usegalaxy.org.au): 58 + Tool usage (5 years) - all main servers: 1165 + Tool usage (all time) (usegalaxy.eu): 349 + Tool usage (all time) (usegalaxy.org): 3067 + Tool usage (all time) (usegalaxy.org.au): 78 + Tool usage (all time) - all main servers: 3494 + ToolShed categories: + - Fasta Manipulation + ToolShed id: fastx_collapser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2017-07-10' + Description: Draw nucleotides distribution chart + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastx_nucleotides_distribution + Galaxy wrapper id: fastx_nucleotides_distribution + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 174 + No. of tool users (5 years) (usegalaxy.org): 4295 + No. of tool users (5 years) (usegalaxy.org.au): 1127 + No. of tool users (5 years) - all main servers: 5596 + No. of tool users (all time) (usegalaxy.eu): 272 + No. of tool users (all time) (usegalaxy.org): 25068 + No. of tool users (all time) (usegalaxy.org.au): 1171 + No. of tool users (all time) - all main servers: 26511 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 61 + Tool usage (5 years) (usegalaxy.org): 1056 + Tool usage (5 years) (usegalaxy.org.au): 70 + Tool usage (5 years) - all main servers: 1187 + Tool usage (all time) (usegalaxy.eu): 92 + Tool usage (all time) (usegalaxy.org): 4180 + Tool usage (all time) (usegalaxy.org.au): 89 + Tool usage (all time) - all main servers: 4361 + ToolShed categories: + - Fastq Manipulation + - Graphics + ToolShed id: fastx_nucleotides_distribution + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2018-04-24' + Description: Compute quality statistics + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastx_quality_statistics + Galaxy wrapper id: fastx_quality_statistics + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 2218 + No. of tool users (5 years) (usegalaxy.org): 20551 + No. of tool users (5 years) (usegalaxy.org.au): 2347 + No. of tool users (5 years) - all main servers: 25116 + No. of tool users (all time) (usegalaxy.eu): 2344 + No. of tool users (all time) (usegalaxy.org): 60032 + No. of tool users (all time) (usegalaxy.org.au): 2460 + No. of tool users (all time) - all main servers: 64836 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 168 + Tool usage (5 years) (usegalaxy.org): 3784 + Tool usage (5 years) (usegalaxy.org.au): 234 + Tool usage (5 years) - all main servers: 4186 + Tool usage (all time) (usegalaxy.eu): 206 + Tool usage (all time) (usegalaxy.org): 9866 + Tool usage (all time) (usegalaxy.org.au): 256 + Tool usage (all time) - all main servers: 10328 + ToolShed categories: + - Fastq Manipulation + - Statistics + ToolShed id: fastx_quality_statistics + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2017-07-10' + Description: Rename sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastx_renamer + Galaxy wrapper id: fastx_renamer + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 2364 + No. of tool users (5 years) (usegalaxy.org): 6572 + No. of tool users (5 years) (usegalaxy.org.au): 462 + No. of tool users (5 years) - all main servers: 9398 + No. of tool users (all time) (usegalaxy.eu): 2526 + No. of tool users (all time) (usegalaxy.org): 11745 + No. of tool users (all time) (usegalaxy.org.au): 696 + No. of tool users (all time) - all main servers: 14967 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 180 + Tool usage (5 years) (usegalaxy.org): 303 + Tool usage (5 years) (usegalaxy.org.au): 49 + Tool usage (5 years) - all main servers: 532 + Tool usage (all time) (usegalaxy.eu): 214 + Tool usage (all time) (usegalaxy.org): 1024 + Tool usage (all time) (usegalaxy.org.au): 64 + Tool usage (all time) - all main servers: 1302 + ToolShed categories: + - Fasta Manipulation + - Fastq Manipulation + ToolShed id: fastx_renamer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2017-07-10' + Description: Reverse-Complement + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastx_reverse_complement + Galaxy wrapper id: fastx_reverse_complement + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 10707 + No. of tool users (5 years) (usegalaxy.org): 21568 + No. of tool users (5 years) (usegalaxy.org.au): 719 + No. of tool users (5 years) - all main servers: 32994 + No. of tool users (all time) (usegalaxy.eu): 12597 + No. of tool users (all time) (usegalaxy.org): 67304 + No. of tool users (all time) (usegalaxy.org.au): 861 + No. of tool users (all time) - all main servers: 80762 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 356 + Tool usage (5 years) (usegalaxy.org): 574 + Tool usage (5 years) (usegalaxy.org.au): 61 + Tool usage (5 years) - all main servers: 991 + Tool usage (all time) (usegalaxy.eu): 415 + Tool usage (all time) (usegalaxy.org): 1527 + Tool usage (all time) (usegalaxy.org.au): 78 + Tool usage (all time) - all main servers: 2020 + ToolShed categories: + - Fastq Manipulation + - Fasta Manipulation + ToolShed id: fastx_reverse_complement + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fastx_toolkit + Conda version: 0.0.14 + Date of first commit of the suite: '2017-07-10' + Description: Trim sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cshl_fastx_trimmer + Galaxy wrapper id: fastx_trimmer + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer + Galaxy wrapper version: 0.0.14 + No. of tool users (5 years) (usegalaxy.eu): 13584 + No. of tool users (5 years) (usegalaxy.org): 123676 + No. of tool users (5 years) (usegalaxy.org.au): 2819 + No. of tool users (5 years) - all main servers: 140079 + No. of tool users (all time) (usegalaxy.eu): 14557 + No. of tool users (all time) (usegalaxy.org): 206733 + No. of tool users (all time) (usegalaxy.org.au): 4757 + No. of tool users (all time) - all main servers: 226047 + Source: http://hannonlab.cshl.edu/fastx_toolkit/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 550 + Tool usage (5 years) (usegalaxy.org): 2034 + Tool usage (5 years) (usegalaxy.org.au): 229 + Tool usage (5 years) - 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fastq_combiner + Galaxy wrapper id: fastq_combiner + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 8604 + No. of tool users (5 years) (usegalaxy.org): 54200 + No. of tool users (5 years) (usegalaxy.org.au): 1562 + No. of tool users (5 years) - all main servers: 64366 + No. of tool users (all time) (usegalaxy.eu): 8799 + No. of tool users (all time) (usegalaxy.org): 75329 + No. of tool users (all time) (usegalaxy.org.au): 1680 + No. of tool users (all time) - all main servers: 85808 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 215 + Tool usage (5 years) (usegalaxy.org): 919 + Tool usage (5 years) (usegalaxy.org.au): 76 + Tool usage (5 years) - 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fastq_groomer + Galaxy wrapper id: fastq_groomer + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 92594 + No. of tool users (5 years) (usegalaxy.org): 179461 + No. of tool users (5 years) (usegalaxy.org.au): 15434 + No. of tool users (5 years) - all main servers: 287489 + No. of tool users (all time) (usegalaxy.eu): 102535 + No. of tool users (all time) (usegalaxy.org): 897457 + No. of tool users (all time) (usegalaxy.org.au): 25533 + No. of tool users (all time) - all main servers: 1025525 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2576 + Tool usage (5 years) (usegalaxy.org): 9437 + Tool usage (5 years) (usegalaxy.org.au): 664 + Tool usage (5 years) - 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fastq_manipulation + Galaxy wrapper id: fastq_manipulation + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 2488 + No. of tool users (5 years) (usegalaxy.org): 6241 + No. of tool users (5 years) (usegalaxy.org.au): 4121 + No. of tool users (5 years) - all main servers: 12850 + No. of tool users (all time) (usegalaxy.eu): 3132 + No. of tool users (all time) (usegalaxy.org): 14508 + No. of tool users (all time) (usegalaxy.org.au): 4592 + No. of tool users (all time) - all main servers: 22232 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 215 + Tool usage (5 years) (usegalaxy.org): 834 + Tool usage (5 years) (usegalaxy.org.au): 131 + Tool usage (5 years) - 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fastq_masker_by_quality + Galaxy wrapper id: fastq_masker_by_quality + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 234 + No. of tool users (5 years) (usegalaxy.org): 2648 + No. of tool users (5 years) (usegalaxy.org.au): 442 + No. of tool users (5 years) - all main servers: 3324 + No. of tool users (all time) (usegalaxy.eu): 249 + No. of tool users (all time) (usegalaxy.org): 8092 + No. of tool users (all time) (usegalaxy.org.au): 466 + No. of tool users (all time) - all main servers: 8807 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 43 + Tool usage (5 years) (usegalaxy.org): 288 + Tool usage (5 years) (usegalaxy.org.au): 12 + Tool usage (5 years) - 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fastq_paired_end_deinterlacer + Galaxy wrapper id: fastq_paired_end_deinterlacer + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 5873 + No. of tool users (5 years) (usegalaxy.org): 14738 + No. of tool users (5 years) (usegalaxy.org.au): 2316 + No. of tool users (5 years) - all main servers: 22927 + No. of tool users (all time) (usegalaxy.eu): 8936 + No. of tool users (all time) (usegalaxy.org): 20229 + No. of tool users (all time) (usegalaxy.org.au): 2711 + No. of tool users (all time) - all main servers: 31876 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 532 + Tool usage (5 years) (usegalaxy.org): 1889 + Tool usage (5 years) (usegalaxy.org.au): 225 + Tool usage (5 years) - 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fastq_paired_end_interlacer + Galaxy wrapper id: fastq_paired_end_interlacer + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 18216 + No. of tool users (5 years) (usegalaxy.org): 23484 + No. of tool users (5 years) (usegalaxy.org.au): 6207 + No. of tool users (5 years) - all main servers: 47907 + No. of tool users (all time) (usegalaxy.eu): 19573 + No. of tool users (all time) (usegalaxy.org): 25936 + No. of tool users (all time) (usegalaxy.org.au): 6551 + No. of tool users (all time) - all main servers: 52060 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2348 + Tool usage (5 years) (usegalaxy.org): 3482 + Tool usage (5 years) (usegalaxy.org.au): 1402 + Tool usage (5 years) - all main servers: 7232 + Tool usage (all time) (usegalaxy.eu): 2492 + Tool usage (all time) (usegalaxy.org): 3851 + Tool usage (all time) (usegalaxy.org.au): 1442 + Tool usage (all time) - all main servers: 7785 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastq_paired_end_interlacer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2019-06-21' + Description: FASTQ joiner on paired end reads + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_paired_end_joiner + Galaxy wrapper id: fastq_paired_end_joiner + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 15628 + No. of tool users (5 years) (usegalaxy.org): 24157 + No. of tool users (5 years) (usegalaxy.org.au): 1941 + No. of tool users (5 years) - all main servers: 41726 + No. of tool users (all time) (usegalaxy.eu): 17130 + No. of tool users (all time) (usegalaxy.org): 58368 + No. of tool users (all time) (usegalaxy.org.au): 2266 + No. of tool users (all time) - all main servers: 77764 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 536 + Tool usage (5 years) (usegalaxy.org): 1954 + Tool usage (5 years) (usegalaxy.org.au): 172 + Tool usage (5 years) - all main servers: 2662 + Tool usage (all time) (usegalaxy.eu): 679 + Tool usage (all time) (usegalaxy.org): 5716 + Tool usage (all time) (usegalaxy.org.au): 214 + Tool usage (all time) - all main servers: 6609 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastq_paired_end_joiner + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2019-06-21' + Description: FASTQ splitter on joined paired end reads + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_paired_end_splitter + Galaxy wrapper id: fastq_paired_end_splitter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 3169 + No. of tool users (5 years) (usegalaxy.org): 19309 + No. of tool users (5 years) (usegalaxy.org.au): 807 + No. of tool users (5 years) - all main servers: 23285 + No. of tool users (all time) (usegalaxy.eu): 3521 + No. of tool users (all time) (usegalaxy.org): 30747 + No. of tool users (all time) (usegalaxy.org.au): 1023 + No. of tool users (all time) - all main servers: 35291 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 459 + Tool usage (5 years) (usegalaxy.org): 1410 + Tool usage (5 years) (usegalaxy.org.au): 219 + Tool usage (5 years) - all main servers: 2088 + Tool usage (all time) (usegalaxy.eu): 535 + Tool usage (all time) (usegalaxy.org): 3441 + Tool usage (all time) (usegalaxy.org.au): 247 + Tool usage (all time) - all main servers: 4223 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastq_paired_end_splitter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2019-06-21' + Description: FASTQ Summary Statistics by column + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_stats + Galaxy wrapper id: fastq_stats + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 3858 + No. of tool users (5 years) (usegalaxy.org): 15213 + No. of tool users (5 years) (usegalaxy.org.au): 3855 + No. of tool users (5 years) - all main servers: 22926 + No. of tool users (all time) (usegalaxy.eu): 4595 + No. of tool users (all time) (usegalaxy.org): 81513 + No. of tool users (all time) (usegalaxy.org.au): 4163 + No. of tool users (all time) - all main servers: 90271 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 680 + Tool usage (5 years) (usegalaxy.org): 3159 + Tool usage (5 years) (usegalaxy.org.au): 184 + Tool usage (5 years) - all main servers: 4023 + Tool usage (all time) (usegalaxy.eu): 815 + Tool usage (all time) (usegalaxy.org): 14109 + Tool usage (all time) (usegalaxy.org.au): 256 + Tool usage (all time) - all main servers: 15180 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastq_stats + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2019-06-21' + Description: FASTQ to Tabular converter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_to_tabular + Galaxy wrapper id: fastq_to_tabular + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 12895 + No. of tool users (5 years) (usegalaxy.org): 13315 + No. of tool users (5 years) (usegalaxy.org.au): 5125 + No. of tool users (5 years) - all main servers: 31335 + No. of tool users (all time) (usegalaxy.eu): 14110 + No. of tool users (all time) (usegalaxy.org): 30673 + No. of tool users (all time) (usegalaxy.org.au): 5373 + No. of tool users (all time) - all main servers: 50156 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 269 + Tool usage (5 years) (usegalaxy.org): 612 + Tool usage (5 years) (usegalaxy.org.au): 64 + Tool usage (5 years) - all main servers: 945 + Tool usage (all time) (usegalaxy.eu): 297 + Tool usage (all time) (usegalaxy.org): 1810 + Tool usage (all time) (usegalaxy.org.au): 87 + Tool usage (all time) - all main servers: 2194 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastq_to_tabular + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2019-06-21' + Description: FASTQ Trimmer by quality + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_trimmer + Galaxy wrapper id: fastq_trimmer + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 10114 + No. of tool users (5 years) (usegalaxy.org): 23906 + No. of tool users (5 years) (usegalaxy.org.au): 1588 + No. of tool users (5 years) - all main servers: 35608 + No. of tool users (all time) (usegalaxy.eu): 11383 + No. of tool users (all time) (usegalaxy.org): 92351 + No. of tool users (all time) (usegalaxy.org.au): 2607 + No. of tool users (all time) - all main servers: 106341 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 582 + Tool usage (5 years) (usegalaxy.org): 1986 + Tool usage (5 years) (usegalaxy.org.au): 108 + Tool usage (5 years) - all main servers: 2676 + Tool usage (all time) (usegalaxy.eu): 665 + Tool usage (all time) (usegalaxy.org): 8818 + Tool usage (all time) (usegalaxy.org.au): 212 + Tool usage (all time) - all main servers: 9695 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastq_trimmer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2019-06-21' + Description: FASTQ to FASTA converter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastq_to_fasta_python + Galaxy wrapper id: fastqtofasta + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 208349 + No. of tool users (5 years) (usegalaxy.org): 131388 + No. of tool users (5 years) (usegalaxy.org.au): 18655 + No. of tool users (5 years) - all main servers: 358392 + No. of tool users (all time) (usegalaxy.eu): 217568 + No. of tool users (all time) (usegalaxy.org): 245005 + No. of tool users (all time) (usegalaxy.org.au): 18655 + No. of tool users (all time) - all main servers: 481228 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3421 + Tool usage (5 years) (usegalaxy.org): 5108 + Tool usage (5 years) (usegalaxy.org.au): 679 + Tool usage (5 years) - all main servers: 9208 + Tool usage (all time) (usegalaxy.eu): 3732 + Tool usage (all time) (usegalaxy.org): 13227 + Tool usage (all time) (usegalaxy.org.au): 679 + Tool usage (all time) - all main servers: 17638 + ToolShed categories: + - Fastq Manipulation + ToolShed id: fastqtofasta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: galaxy_sequence_utils + Conda version: 1.2.0 + Date of first commit of the suite: '2019-06-21' + Description: Tabular to FASTQ converter + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tabular_to_fastq + Galaxy wrapper id: tabular_to_fastq + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq + Galaxy wrapper version: 1.1.5 + No. of tool users (5 years) (usegalaxy.eu): 7011 + No. of tool users (5 years) (usegalaxy.org): 9473 + No. of tool users (5 years) (usegalaxy.org.au): 850 + No. of tool users (5 years) - all main servers: 17334 + No. of tool users (all time) (usegalaxy.eu): 8135 + No. of tool users (all time) (usegalaxy.org): 28494 + No. of tool users (all time) (usegalaxy.org.au): 1090 + No. of tool users (all time) - all main servers: 37719 + Source: https://github.com/galaxyproject/sequence_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 449 + Tool usage (5 years) (usegalaxy.org): 626 + Tool usage (5 years) (usegalaxy.org.au): 80 + Tool usage (5 years) - all main servers: 1155 + Tool usage (all time) (usegalaxy.eu): 482 + Tool usage (all time) (usegalaxy.org): 2183 + Tool usage (all time) (usegalaxy.org.au): 104 + Tool usage (all time) - all main servers: 2769 + ToolShed categories: + - Fastq Manipulation + ToolShed id: tabular_to_fastq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: kraken + Conda version: 1.1.1 + Date of first commit of the suite: '2017-01-24' + Description: Kraken is a system for assigning taxonomic labels to short DNAsequences, + usually obtained through metagenomic studies. Previous attempts by otherbioinformatics + software to accomplish this task have often used sequence alignmentor machine + learning techniques that were quite slow, leading to the developmentof less sensitive + but much faster abundance estimation programs. Kraken aims toachieve high sensitivity + and high speed by utilizing exact alignments of k-mersand a novel classification + algorithm. + EDAM operation: + - Taxonomic classification + EDAM operation (no superclasses): + - Taxonomic classification + EDAM topic: + - Taxonomy + - Metagenomics + EDAM topic (no superclasses): + - Taxonomy + - Metagenomics + Galaxy tool ids: + - kraken-filter + - kraken-mpa-report + - kraken-report + - kraken-translate + - kraken + Galaxy wrapper id: kraken + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 48136 + No. of tool users (5 years) (usegalaxy.org): 59952 + No. of tool users (5 years) (usegalaxy.org.au): 29008 + No. of tool users (5 years) - all main servers: 137096 + No. of tool users (all time) (usegalaxy.eu): 48164 + No. of tool users (all time) (usegalaxy.org): 130398 + No. of tool users (all time) (usegalaxy.org.au): 31148 + No. of tool users (all time) - all main servers: 209710 + Source: http://ccb.jhu.edu/software/kraken/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2754 + Tool usage (5 years) (usegalaxy.org): 5869 + Tool usage (5 years) (usegalaxy.org.au): 1936 + Tool usage (5 years) - all main servers: 10559 + Tool usage (all time) (usegalaxy.eu): 2760 + Tool usage (all time) (usegalaxy.org): 8654 + Tool usage (all time) (usegalaxy.org.au): 2200 + Tool usage (all time) - all main servers: 13614 + ToolShed categories: + - Metagenomics + ToolShed id: kraken + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 2 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 2 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: System for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other bioinformatics + software to accomplish this task have often used sequence alignment or machine + learning techniques that were quite slow, leading to the development of less sensitive + but much faster abundance estimation programs. It aims to achieve high sensitivity + and high speed by utilizing exact alignments of k-mers and a novel classification + algorithm. + bio.tool id: kraken + bio.tool ids: + - kraken + bio.tool name: Kraken +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: kraken2 + Conda version: 2.1.3 + Date of first commit of the suite: '2019-03-06' + Description: Kraken2 for taxonomic designation. + EDAM operation: + - Taxonomic classification + EDAM operation (no superclasses): + - Taxonomic classification + EDAM topic: + - Taxonomy + - Metagenomics + EDAM topic (no superclasses): + - Taxonomy + - Metagenomics + Galaxy tool ids: + - kraken2 + Galaxy wrapper id: kraken2 + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ + Galaxy wrapper version: 2.1.3 + No. of tool users (5 years) (usegalaxy.eu): 271367 + No. of tool users (5 years) (usegalaxy.org): 101752 + No. of tool users (5 years) (usegalaxy.org.au): 53562 + No. of tool users (5 years) - all main servers: 426681 + No. of tool users (all time) (usegalaxy.eu): 271786 + No. of tool users (all time) (usegalaxy.org): 101752 + No. of tool users (all time) (usegalaxy.org.au): 53562 + No. of tool users (all time) - all main servers: 427100 + Source: http://ccb.jhu.edu/software/kraken/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 6384 + Tool usage (5 years) (usegalaxy.org): 4662 + Tool usage (5 years) (usegalaxy.org.au): 1663 + Tool usage (5 years) - all main servers: 12709 + Tool usage (all time) (usegalaxy.eu): 6409 + Tool usage (all time) (usegalaxy.org): 4662 + Tool usage (all time) (usegalaxy.org.au): 1663 + Tool usage (all time) - all main servers: 12734 + ToolShed categories: + - Metagenomics + ToolShed id: kraken2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 1 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 1 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Kraken 2 is the newest version of Kraken, a taxonomic classification + system using exact k-mer matches to achieve high accuracy and fast classification + speeds. This classifier matches each k-mer within a query sequence to the lowest + common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments + inform the classification algorithm. + bio.tool id: kraken2 + bio.tool ids: + - kraken2 + bio.tool name: kraken2 +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: samtools + Conda version: '1.21' + Date of first commit of the suite: '2021-01-04' + Description: null + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: [] + Galaxy wrapper id: samtools + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools + Galaxy wrapper version: '1.20' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/samtools/samtools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - SAM + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 5 + Conda id: biopython + Conda version: '1.70' + Date of first commit of the suite: '2018-07-06' + Description: SnpEff is a genetic variant annotation and effect prediction toolbox + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - snpEff + - snpEff_build_gb + - snpEff_databases + - snpEff_download + - snpEff_get_chr_names + Galaxy wrapper id: snpeff + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 103826 + No. of tool users (5 years) (usegalaxy.org): 115727 + No. of tool users (5 years) (usegalaxy.org.au): 11817 + No. of tool users (5 years) - all main servers: 231370 + No. of tool users (all time) (usegalaxy.eu): 108296 + No. of tool users (all time) (usegalaxy.org): 178110 + No. of tool users (all time) (usegalaxy.org.au): 13155 + No. of tool users (all time) - all main servers: 299561 + Source: http://snpeff.sourceforge.net/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7181 + Tool usage (5 years) (usegalaxy.org): 15871 + Tool usage (5 years) (usegalaxy.org.au): 2148 + Tool usage (5 years) - all main servers: 25200 + Tool usage (all time) (usegalaxy.eu): 7908 + Tool usage (all time) (usegalaxy.org): 22769 + Tool usage (all time) (usegalaxy.org.au): 2321 + Tool usage (all time) - all main servers: 32998 + ToolShed categories: + - Genome-Wide Association Study + - Variant Analysis + ToolShed id: snpeff + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 1 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 5 + Tools available on GalaxyTrakr: 5 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 5 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 5 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 5 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 5 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 8 + Available on UseGalaxy.fr: 8 + Available on UseGalaxy.org (Main): 8 + Available on UseGalaxy.org.au: 8 + Conda id: snpsift + Conda version: '5.2' + Date of first commit of the suite: '2015-04-01' + Description: snpEff SnpSift tools from Pablo Cingolani + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - snpSift_annotate + - snpSift_caseControl + - snpSift_extractFields + - snpSift_filter + - snpSift_int + - snpSift_rmInfo + - snpsift_vartype + - snpSift_vcfCheck + Galaxy wrapper id: snpsift + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 5142904 + No. of tool users (5 years) (usegalaxy.org): 382391 + No. of tool users (5 years) (usegalaxy.org.au): 104030 + No. of tool users (5 years) - all main servers: 5629325 + No. of tool users (all time) (usegalaxy.eu): 5146618 + No. of tool users (all time) (usegalaxy.org): 421190 + No. of tool users (all time) (usegalaxy.org.au): 105024 + No. of tool users (all time) - all main servers: 5672832 + Source: http://snpeff.sourceforge.net/SnpSift.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3602 + Tool usage (5 years) (usegalaxy.org): 7013 + Tool usage (5 years) (usegalaxy.org.au): 960 + Tool usage (5 years) - all main servers: 11575 + Tool usage (all time) (usegalaxy.eu): 4283 + Tool usage (all time) (usegalaxy.org): 9678 + Tool usage (all time) (usegalaxy.org.au): 1184 + Tool usage (all time) - all main servers: 15145 + ToolShed categories: + - Variant Analysis + ToolShed id: snpsift + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 8 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 8 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 8 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 8 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 8 + Tools available on UseGalaxy.cz: 8 + Tools available on UseGalaxy.eu: 8 + Tools available on UseGalaxy.fr: 8 + Tools available on UseGalaxy.no: 8 + Tools available on UseGalaxy.org (Main): 8 + Tools available on UseGalaxy.org.au: 8 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 8 + UseGalaxy.cz: 8 + UseGalaxy.eu: 8 + UseGalaxy.fr: 8 + UseGalaxy.no: 8 + UseGalaxy.or: 8 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: snpsift + Conda version: '5.2' + Date of first commit of the suite: '2014-11-11' + Description: snpEff SnpSift dbnsfp tool from Pablo Cingolani + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - snpSift_dbnsfp + Galaxy wrapper id: snpsift_dbnsfp + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 52 + No. of tool users (5 years) (usegalaxy.org): 421 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 473 + No. of tool users (all time) (usegalaxy.eu): 55 + No. of tool users (all time) (usegalaxy.org): 421 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 476 + Source: http://snpeff.sourceforge.net/SnpSift.html#dbNSFP + Status: To update + Tool usage (5 years) (usegalaxy.eu): 23 + Tool usage (5 years) (usegalaxy.org): 75 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 98 + Tool usage (all time) (usegalaxy.eu): 24 + Tool usage (all time) (usegalaxy.org): 75 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 99 + ToolShed categories: + - Variant Analysis + ToolShed id: snpsift_dbnsfp + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: snpsift + Conda version: '5.2' + Date of first commit of the suite: '2014-11-11' + Description: Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, + Reactome + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - snpSift_geneSets + Galaxy wrapper id: snpsift_genesets + Galaxy wrapper owner: iuc + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 509 + No. of tool users (5 years) (usegalaxy.org): 474 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 983 + No. of tool users (all time) (usegalaxy.eu): 554 + No. of tool users (all time) (usegalaxy.org): 474 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1028 + Source: http://snpeff.sourceforge.net/SnpSift.html#geneSets + Status: To update + Tool usage (5 years) (usegalaxy.eu): 107 + Tool usage (5 years) (usegalaxy.org): 190 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 297 + Tool usage (all time) (usegalaxy.eu): 128 + Tool usage (all time) (usegalaxy.org): 190 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 318 + ToolShed categories: + - Variant Analysis + ToolShed id: snpsift_genesets + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Converts VCF files into tab-delimited format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcf2tsv + Galaxy wrapper id: vcf2tsv + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 169090 + No. of tool users (5 years) (usegalaxy.org): 16304 + No. of tool users (5 years) (usegalaxy.org.au): 2485 + No. of tool users (5 years) - all main servers: 187879 + No. of tool users (all time) (usegalaxy.eu): 169679 + No. of tool users (all time) (usegalaxy.org): 42215 + No. of tool users (all time) (usegalaxy.org.au): 2511 + No. of tool users (all time) - all main servers: 214405 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 823 + Tool usage (5 years) (usegalaxy.org): 1141 + Tool usage (5 years) (usegalaxy.org.au): 169 + Tool usage (5 years) - all main servers: 2133 + Tool usage (all time) (usegalaxy.eu): 874 + Tool usage (all time) (usegalaxy.org): 2594 + Tool usage (all time) (usegalaxy.org.au): 172 + Tool usage (all time) - all main servers: 3640 + ToolShed categories: + - Variant Analysis + - Convert Formats + ToolShed id: vcf2tsv + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 1 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Adds info fields from the second dataset which are not present in the + first dataset. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - 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all main servers: 152 + ToolShed categories: + - Variant Analysis + ToolShed id: vcfaddinfo + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Splits alleleic primitives (gaps or mismatches) into multiple VCF lines + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcfallelicprimitives + Galaxy wrapper id: vcfallelicprimitives + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 6879 + No. of tool users (5 years) (usegalaxy.org): 7585 + No. of tool users (5 years) (usegalaxy.org.au): 1648 + No. of tool users (5 years) - all main servers: 16112 + No. of tool users (all time) (usegalaxy.eu): 17157 + No. of tool users (all time) (usegalaxy.org): 14509 + No. of tool users (all time) (usegalaxy.org.au): 1681 + No. of tool users (all time) - all main servers: 33347 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 897 + Tool usage (5 years) (usegalaxy.org): 1245 + Tool usage (5 years) (usegalaxy.org.au): 225 + Tool usage (5 years) - 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vcfannotate + Galaxy wrapper id: vcfannotate + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 2797 + No. of tool users (5 years) (usegalaxy.org): 3668 + No. of tool users (5 years) (usegalaxy.org.au): 494 + No. of tool users (5 years) - all main servers: 6959 + No. of tool users (all time) (usegalaxy.eu): 2850 + No. of tool users (all time) (usegalaxy.org): 14532 + No. of tool users (all time) (usegalaxy.org.au): 507 + No. of tool users (all time) - all main servers: 17889 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 157 + Tool usage (5 years) (usegalaxy.org): 652 + Tool usage (5 years) (usegalaxy.org.au): 61 + Tool usage (5 years) - all main servers: 870 + Tool usage (all time) (usegalaxy.eu): 181 + Tool usage (all time) (usegalaxy.org): 1392 + Tool usage (all time) (usegalaxy.org.au): 63 + Tool usage (all time) - all main servers: 1636 + ToolShed categories: + - Variant Analysis + ToolShed id: vcfannotate + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Annotate genotypes in a VCF dataset using genotypes from another VCF + dataset. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcfannotategenotypes + Galaxy wrapper id: vcfannotategenotypes + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 189 + No. of tool users (5 years) (usegalaxy.org): 497 + No. of tool users (5 years) (usegalaxy.org.au): 184 + No. of tool users (5 years) - all main servers: 870 + No. of tool users (all time) (usegalaxy.eu): 203 + No. of tool users (all time) (usegalaxy.org): 1828 + No. of tool users (all time) (usegalaxy.org.au): 197 + No. of tool users (all time) - all main servers: 2228 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 62 + Tool usage (5 years) (usegalaxy.org): 155 + Tool usage (5 years) (usegalaxy.org.au): 11 + Tool usage (5 years) - 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vcfbedintersect + Galaxy wrapper id: vcfbedintersect + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 3017 + No. of tool users (5 years) (usegalaxy.org): 4709 + No. of tool users (5 years) (usegalaxy.org.au): 507 + No. of tool users (5 years) - all main servers: 8233 + No. of tool users (all time) (usegalaxy.eu): 4049 + No. of tool users (all time) (usegalaxy.org): 20250 + No. of tool users (all time) (usegalaxy.org.au): 527 + No. of tool users (all time) - all main servers: 24826 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 185 + Tool usage (5 years) (usegalaxy.org): 406 + Tool usage (5 years) (usegalaxy.org.au): 40 + Tool usage (5 years) - 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vcfbreakcreatemulti + Galaxy wrapper id: vcfbreakcreatemulti + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 416 + No. of tool users (5 years) (usegalaxy.org): 3969 + No. of tool users (5 years) (usegalaxy.org.au): 362 + No. of tool users (5 years) - all main servers: 4747 + No. of tool users (all time) (usegalaxy.eu): 478 + No. of tool users (all time) (usegalaxy.org): 10457 + No. of tool users (all time) (usegalaxy.org.au): 378 + No. of tool users (all time) - all main servers: 11313 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 35 + Tool usage (5 years) (usegalaxy.org): 82 + Tool usage (5 years) (usegalaxy.org.au): 8 + Tool usage (5 years) - 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vcfcheck + Galaxy wrapper id: vcfcheck + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 745 + No. of tool users (5 years) (usegalaxy.org): 803 + No. of tool users (5 years) (usegalaxy.org.au): 241 + No. of tool users (5 years) - all main servers: 1789 + No. of tool users (all time) (usegalaxy.eu): 767 + No. of tool users (all time) (usegalaxy.org): 1895 + No. of tool users (all time) (usegalaxy.org.au): 256 + No. of tool users (all time) - all main servers: 2918 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 96 + Tool usage (5 years) (usegalaxy.org): 222 + Tool usage (5 years) (usegalaxy.org.au): 16 + Tool usage (5 years) - all main servers: 334 + Tool usage (all time) (usegalaxy.eu): 106 + Tool usage (all time) (usegalaxy.org): 627 + Tool usage (all time) (usegalaxy.org.au): 17 + Tool usage (all time) - all main servers: 750 + ToolShed categories: + - Variant Analysis + ToolShed id: vcfcheck + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Combine multiple VCF datasets + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcfcombine + Galaxy wrapper id: vcfcombine + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 1422 + No. of tool users (5 years) (usegalaxy.org): 4951 + No. of tool users (5 years) (usegalaxy.org.au): 493 + No. of tool users (5 years) - all main servers: 6866 + No. of tool users (all time) (usegalaxy.eu): 2020 + No. of tool users (all time) (usegalaxy.org): 19530 + No. of tool users (all time) (usegalaxy.org.au): 516 + No. of tool users (all time) - all main servers: 22066 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 284 + Tool usage (5 years) (usegalaxy.org): 1021 + Tool usage (5 years) (usegalaxy.org.au): 60 + Tool usage (5 years) - all main servers: 1365 + Tool usage (all time) (usegalaxy.eu): 505 + Tool usage (all time) (usegalaxy.org): 2669 + Tool usage (all time) (usegalaxy.org.au): 62 + Tool usage (all time) - all main servers: 3236 + ToolShed categories: + - Variant Analysis + ToolShed id: vcfcombine + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Output records belonging to samples commong between two datasets. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcfcommonsamples + Galaxy wrapper id: vcfcommonsamples + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 233 + No. of tool users (5 years) (usegalaxy.org): 234 + No. of tool users (5 years) (usegalaxy.org.au): 199 + No. of tool users (5 years) - all main servers: 666 + No. of tool users (all time) (usegalaxy.eu): 253 + No. of tool users (all time) (usegalaxy.org): 1839 + No. of tool users (all time) (usegalaxy.org.au): 214 + No. of tool users (all time) - all main servers: 2306 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 37 + Tool usage (5 years) (usegalaxy.org): 79 + Tool usage (5 years) (usegalaxy.org.au): 11 + Tool usage (5 years) - all main servers: 127 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 287 + Tool usage (all time) (usegalaxy.org.au): 12 + Tool usage (all time) - all main servers: 341 + ToolShed categories: + - Variant Analysis + ToolShed id: vcfcommonsamples + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Calculate distance to the nearest variant. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcfdistance + Galaxy wrapper id: vcfdistance + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 572 + No. of tool users (5 years) (usegalaxy.org): 2063 + No. of tool users (5 years) (usegalaxy.org.au): 272 + No. of tool users (5 years) - all main servers: 2907 + No. of tool users (all time) (usegalaxy.eu): 585 + No. of tool users (all time) (usegalaxy.org): 2427 + No. of tool users (all time) (usegalaxy.org.au): 290 + No. of tool users (all time) - all main servers: 3302 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 90 + Tool usage (5 years) (usegalaxy.org): 139 + Tool usage (5 years) (usegalaxy.org.au): 19 + Tool usage (5 years) - all main servers: 248 + Tool usage (all time) (usegalaxy.eu): 92 + Tool usage (all time) (usegalaxy.org): 296 + Tool usage (all time) (usegalaxy.org.au): 22 + Tool usage (all time) - all main servers: 410 + ToolShed categories: + - Variant Analysis + ToolShed id: vcfdistance + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Tool for filtering VCF files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcffilter2 + Galaxy wrapper id: vcffilter + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 37489 + No. of tool users (5 years) (usegalaxy.org): 75128 + No. of tool users (5 years) (usegalaxy.org.au): 2626 + No. of tool users (5 years) - all main servers: 115243 + No. of tool users (all time) (usegalaxy.eu): 47142 + No. of tool users (all time) (usegalaxy.org): 162296 + No. of tool users (all time) (usegalaxy.org.au): 2736 + No. of tool users (all time) - all main servers: 212174 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2113 + Tool usage (5 years) (usegalaxy.org): 5730 + Tool usage (5 years) (usegalaxy.org.au): 320 + Tool usage (5 years) - all main servers: 8163 + Tool usage (all time) (usegalaxy.eu): 2218 + Tool usage (all time) (usegalaxy.org): 10533 + Tool usage (all time) (usegalaxy.org.au): 331 + Tool usage (all time) - all main servers: 13082 + ToolShed categories: + - Variant Analysis + ToolShed id: vcffilter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Count the allele frequencies across alleles present in each record + in the VCF file. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcffixup + Galaxy wrapper id: vcffixup + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 926 + No. of tool users (5 years) (usegalaxy.org): 2291 + No. of tool users (5 years) (usegalaxy.org.au): 251 + No. of tool users (5 years) - all main servers: 3468 + No. of tool users (all time) (usegalaxy.eu): 957 + No. of tool users (all time) (usegalaxy.org): 5323 + No. of tool users (all time) (usegalaxy.org.au): 265 + No. of tool users (all time) - all main servers: 6545 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 155 + Tool usage (5 years) (usegalaxy.org): 313 + Tool usage (5 years) (usegalaxy.org.au): 28 + Tool usage (5 years) - all main servers: 496 + Tool usage (all time) (usegalaxy.eu): 173 + Tool usage (all time) (usegalaxy.org): 985 + Tool usage (all time) (usegalaxy.org.au): 31 + Tool usage (all time) - all main servers: 1189 + ToolShed categories: + - Variant Analysis + ToolShed id: vcffixup + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Removes multi-allelic sites by picking the most common alternate + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcfflatten2 + Galaxy wrapper id: vcfflatten + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 172 + No. of tool users (5 years) (usegalaxy.org): 351 + No. of tool users (5 years) (usegalaxy.org.au): 312 + No. of tool users (5 years) - all main servers: 835 + No. of tool users (all time) (usegalaxy.eu): 183 + No. of tool users (all time) (usegalaxy.org): 879 + No. of tool users (all time) (usegalaxy.org.au): 342 + No. of tool users (all time) - all main servers: 1404 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 21 + Tool usage (5 years) (usegalaxy.org): 67 + Tool usage (5 years) (usegalaxy.org.au): 15 + Tool usage (5 years) - all main servers: 103 + Tool usage (all time) (usegalaxy.eu): 25 + Tool usage (all time) (usegalaxy.org): 201 + Tool usage (all time) (usegalaxy.org.au): 16 + Tool usage (all time) - all main servers: 242 + ToolShed categories: + - Variant Analysis + ToolShed id: vcfflatten + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: vcflib + Conda version: 1.0.10 + Date of first commit of the suite: '2017-01-24' + Description: Convert genotype-based phased alleles into haplotype alleles + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vcfgeno2haplo + Galaxy wrapper id: vcfgeno2haplo + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 778 + No. of tool users (5 years) (usegalaxy.org): 2414 + No. of tool users (5 years) (usegalaxy.org.au): 209 + No. of tool users (5 years) - all main servers: 3401 + No. of tool users (all time) (usegalaxy.eu): 794 + No. of tool users (all time) (usegalaxy.org): 3721 + No. of tool users (all time) (usegalaxy.org.au): 225 + No. of tool users (all time) - all main servers: 4740 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 107 + Tool usage (5 years) (usegalaxy.org): 179 + Tool usage (5 years) (usegalaxy.org.au): 20 + Tool usage (5 years) - all main servers: 306 + Tool usage (all time) (usegalaxy.eu): 112 + Tool usage (all time) (usegalaxy.org): 508 + Tool usage (all time) (usegalaxy.org.au): 21 + Tool usage (all time) - 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vcfleftalign + Galaxy wrapper id: vcfleftalign + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 269 + No. of tool users (5 years) (usegalaxy.org): 358 + No. of tool users (5 years) (usegalaxy.org.au): 179 + No. of tool users (5 years) - all main servers: 806 + No. of tool users (all time) (usegalaxy.eu): 310 + No. of tool users (all time) (usegalaxy.org): 1071 + No. of tool users (all time) (usegalaxy.org.au): 213 + No. of tool users (all time) - all main servers: 1594 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 38 + Tool usage (5 years) (usegalaxy.org): 89 + Tool usage (5 years) (usegalaxy.org.au): 12 + Tool usage (5 years) - all main servers: 139 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 287 + Tool usage (all time) (usegalaxy.org.au): 14 + Tool usage (all time) - 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vcfprimers + Galaxy wrapper id: vcfprimers + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 590 + No. of tool users (5 years) (usegalaxy.org): 403 + No. of tool users (5 years) (usegalaxy.org.au): 190 + No. of tool users (5 years) - all main servers: 1183 + No. of tool users (all time) (usegalaxy.eu): 711 + No. of tool users (all time) (usegalaxy.org): 831 + No. of tool users (all time) (usegalaxy.org.au): 214 + No. of tool users (all time) - all main servers: 1756 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 28 + Tool usage (5 years) (usegalaxy.org): 75 + Tool usage (5 years) (usegalaxy.org.au): 10 + Tool usage (5 years) - all main servers: 113 + Tool usage (all time) (usegalaxy.eu): 33 + Tool usage (all time) (usegalaxy.org): 200 + Tool usage (all time) (usegalaxy.org.au): 12 + Tool usage (all time) - 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vcfrandomsample + Galaxy wrapper id: vcfrandomsample + Galaxy wrapper owner: devteam + Galaxy wrapper parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 161 + No. of tool users (5 years) (usegalaxy.org): 153 + No. of tool users (5 years) (usegalaxy.org.au): 184 + No. of tool users (5 years) - all main servers: 498 + No. of tool users (all time) (usegalaxy.eu): 168 + No. of tool users (all time) (usegalaxy.org): 350 + No. of tool users (all time) (usegalaxy.org.au): 192 + No. of tool users (all time) - all main servers: 710 + Source: https://github.com/ekg/vcflib + Status: To update + Tool usage (5 years) (usegalaxy.eu): 13 + Tool usage (5 years) (usegalaxy.org): 27 + Tool usage (5 years) (usegalaxy.org.au): 6 + Tool usage (5 years) - all main servers: 46 + Tool usage (all time) (usegalaxy.eu): 15 + Tool usage (all time) (usegalaxy.org): 75 + Tool usage (all time) (usegalaxy.org.au): 6 + Tool usage (all time) - 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calisp + Galaxy wrapper id: calisp + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp + Galaxy wrapper version: 3.0.13 + No. of tool users (5 years) (usegalaxy.eu): 2 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2 + No. of tool users (all time) (usegalaxy.eu): 2 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2 + Source: https://github.com/kinestetika/Calisp/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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cardinal_classification + - cardinal_colocalization + - cardinal_combine + - cardinal_data_exporter + - cardinal_filtering + - cardinal_mz_images + - cardinal_preprocessing + - cardinal_quality_report + - cardinal_segmentations + - cardinal_single_ion_segmentation + - cardinal_spectra_plots + Galaxy wrapper id: cardinal + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal + Galaxy wrapper version: 3.4.3 + No. of tool users (5 years) (usegalaxy.eu): 41875 + No. of tool users (5 years) (usegalaxy.org): 12 + No. of tool users (5 years) (usegalaxy.org.au): 7512 + No. of tool users (5 years) - all main servers: 49399 + No. of tool users (all time) (usegalaxy.eu): 50702 + No. of tool users (all time) (usegalaxy.org): 12 + No. of tool users (all time) (usegalaxy.org.au): 7512 + No. of tool users (all time) - all main servers: 58226 + Source: http://cardinalmsi.org + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 663 + Tool usage (5 years) (usegalaxy.org): 1 + Tool usage (5 years) (usegalaxy.org.au): 231 + Tool usage (5 years) - all main servers: 895 + Tool usage (all time) (usegalaxy.eu): 713 + Tool usage (all time) (usegalaxy.org): 1 + Tool usage (all time) (usegalaxy.org.au): 231 + Tool usage (all time) - all main servers: 945 + ToolShed categories: + - Proteomics + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 9 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 9 + Tools available on UseGalaxy.cz: 11 + Tools available on UseGalaxy.eu: 11 + Tools available on UseGalaxy.fr: 11 + Tools available on UseGalaxy.no: 9 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 9 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 9 + UseGalaxy.cz: 11 + UseGalaxy.eu: 11 + UseGalaxy.fr: 9 + UseGalaxy.no: 9 + UseGalaxy.or: 9 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: wget + Conda version: null + Date of first commit of the suite: '2015-01-24' + Description: Protein Database Downloader + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - dbbuilder + Galaxy wrapper id: dbbuilder + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder + Galaxy wrapper version: 0.3.4 + No. of tool users (5 years) (usegalaxy.eu): 4813 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 961 + No. of tool users (5 years) - all main servers: 5774 + No. of tool users (all time) (usegalaxy.eu): 5555 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 961 + No. of tool users (all time) - all main servers: 6516 + Source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder + Status: To update + Tool usage (5 years) (usegalaxy.eu): 687 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 87 + Tool usage (5 years) - all main servers: 774 + Tool usage (all time) (usegalaxy.eu): 805 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 87 + Tool usage (all time) - all main servers: 892 + ToolShed categories: + - Proteomics + ToolShed id: dbbuilder + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2015-01-24' + Description: Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: [] + Galaxy wrapper id: decoyfasta + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Proteomics + ToolShed id: decoyfasta + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: dia_umpire + Conda version: 2.1.6 + Date of first commit of the suite: '2015-08-26' + Description: DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based + proteomics + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - dia_umpire_se + Galaxy wrapper id: dia_umpire + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire + Galaxy wrapper version: 2.1.3 + No. of tool users (5 years) (usegalaxy.eu): 28 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 134 + No. of tool users (5 years) - all main servers: 162 + No. of tool users (all time) (usegalaxy.eu): 33 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 134 + No. of tool users (all time) - all main servers: 167 + Source: http://diaumpire.sourceforge.net/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Proteomics + ToolShed id: dia_umpire + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-dialignr + Conda version: 2.10.0 + Date of first commit of the suite: '2020-12-23' + Description: DIAlignR is an R package for retention time alignment of targeted mass + spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 + chromatograms directly and uses dynamic programming for alignment of raw chromatographic + traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw + data-based) alignment to establish correspondence between peaks. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - dialignr + Galaxy wrapper id: dialignr + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 40 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 40 + No. of tool users (all time) (usegalaxy.eu): 40 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 40 + Source: https://github.com/shubham1637/DIAlignR + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Proteomics + ToolShed id: dialignr + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-06-26' + Description: DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data + processing. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - diann + Galaxy wrapper id: diann + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann + Galaxy wrapper source: https://github.com/vdemichev/DiaNN + Galaxy wrapper version: 1.8.1 + No. of tool users (5 years) (usegalaxy.eu): 72 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 171 + No. of tool users (5 years) - all main servers: 243 + No. of tool users (all time) (usegalaxy.eu): 72 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 171 + No. of tool users (all time) - all main servers: 243 + Source: https://github.com/vdemichev/DiaNN + Status: To update + Tool usage (5 years) (usegalaxy.eu): 14 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 14 + Tool usage (5 years) - all main servers: 28 + Tool usage (all time) (usegalaxy.eu): 14 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 14 + Tool usage (all time) - all main servers: 28 + ToolShed categories: + - Proteomics + ToolShed id: diann + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: diapysef + Conda version: 1.0.10 + Date of first commit of the suite: '2020-02-27' + Description: diapysef is a convenience package for working with DIA-PASEF data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - diapysef + Galaxy wrapper id: diapysef + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef + Galaxy wrapper source: https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef + Galaxy wrapper version: 0.3.5.0 + No. of tool users (5 years) (usegalaxy.eu): 262 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 256 + No. of tool users (5 years) - all main servers: 518 + No. of tool users (all time) (usegalaxy.eu): 262 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 256 + No. of tool users (all time) - all main servers: 518 + Source: https://pypi.org/project/diapysef/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 38 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 6 + Tool usage (5 years) - all main servers: 44 + Tool usage (all time) (usegalaxy.eu): 38 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 6 + Tool usage (all time) - all main servers: 44 + ToolShed categories: + - Proteomics + ToolShed id: diapysef + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: diffacto + Conda version: 1.0.7 + Date of first commit of the suite: '2021-06-20' + Description: Diffacto comparative protein abundance estimation + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - diffacto + Galaxy wrapper id: diffacto + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto + Galaxy wrapper version: 1.0.6 + No. of tool users (5 years) (usegalaxy.eu): 11 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 11 + No. of tool users (all time) (usegalaxy.eu): 11 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 11 + Source: https://github.com/statisticalbiotechnology/diffacto + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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It uses precomputed orthologous groups and phylogenies from the + eggNOG database (http://eggnog5.embl.de) to transfer functional information from + fine-grained orthologs only. + bio.tool id: eggnog-mapper-v2 + bio.tool ids: + - eggnog-mapper-v2 + bio.tool name: eggNOG-mapper v2 +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 4 + Conda id: encyclopedia + Conda version: 2.12.30 + Date of first commit of the suite: '2020-09-11' + Description: Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - encyclopedia_encyclopedia + - encyclopedia_fasta_to_prosit_csv + - encyclopedia_library_to_blib + - encyclopedia_prosit_csv_to_library + - encyclopedia_quantify + - encyclopedia_searchtolib + - encyclopedia_walnut + Galaxy wrapper id: encyclopedia + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia + Galaxy wrapper version: 1.12.34 + No. of tool users (5 years) (usegalaxy.eu): 738 + No. of tool users (5 years) (usegalaxy.org): 1 + No. of tool users (5 years) (usegalaxy.org.au): 42 + No. of tool users (5 years) - 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fasta_merge_files_and_filter_unique_sequences + Galaxy wrapper id: fasta_merge_files_and_filter_unique_sequences + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences + Galaxy wrapper version: 1.2.0 + No. of tool users (5 years) (usegalaxy.eu): 30917 + No. of tool users (5 years) (usegalaxy.org): 36869 + No. of tool users (5 years) (usegalaxy.org.au): 5236 + No. of tool users (5 years) - all main servers: 73022 + No. of tool users (all time) (usegalaxy.eu): 32191 + No. of tool users (all time) (usegalaxy.org): 36869 + No. of tool users (all time) (usegalaxy.org.au): 5236 + No. of tool users (all time) - all main servers: 74296 + Source: https://github.com/galaxyproteomics/tools-galaxyp/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1142 + Tool usage (5 years) (usegalaxy.org): 1346 + Tool usage (5 years) (usegalaxy.org.au): 230 + Tool usage (5 years) - all main servers: 2718 + Tool usage (all time) (usegalaxy.eu): 1257 + Tool usage (all time) (usegalaxy.org): 1346 + Tool usage (all time) (usegalaxy.org.au): 230 + Tool usage (all time) - all main servers: 2833 + ToolShed categories: + - Fasta Manipulation + ToolShed id: fasta_merge_files_and_filter_unique_sequences + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-07-23' + Description: Generate FASTA from FASTG + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fastg2protlib-peptides + - fastg2protlib-validate + Galaxy wrapper id: fastg2protlib + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 29 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 29 + No. of tool users (all time) (usegalaxy.eu): 29 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 29 + Source: https://github.com/galaxyproteomics/fastg2protlib.git + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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feature_alignment + Galaxy wrapper id: feature_alignment + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment + Galaxy wrapper source: https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md + Galaxy wrapper version: 0.11.0 + No. of tool users (5 years) (usegalaxy.eu): 18 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 18 + No. of tool users (all time) (usegalaxy.eu): 18 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 18 + Source: null + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Proteomics + ToolShed id: feature_alignment + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2015-01-24' + Description: Filter FASTA on the headers and/or the sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - filter_by_fasta_ids + Galaxy wrapper id: filter_by_fasta_ids + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids + Galaxy wrapper version: '2.3' + No. of tool users (5 years) (usegalaxy.eu): 26717 + No. of tool users (5 years) (usegalaxy.org): 42990 + No. of tool users (5 years) (usegalaxy.org.au): 9619 + No. of tool users (5 years) - all main servers: 79326 + No. of tool users (all time) (usegalaxy.eu): 29932 + No. of tool users (all time) (usegalaxy.org): 42990 + No. of tool users (all time) (usegalaxy.org.au): 9619 + No. of tool users (all time) - all main servers: 82541 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1026 + Tool usage (5 years) (usegalaxy.org): 1176 + Tool usage (5 years) (usegalaxy.org.au): 230 + Tool usage (5 years) - all main servers: 2432 + Tool usage (all time) (usegalaxy.eu): 1072 + Tool usage (all time) (usegalaxy.org): 1176 + Tool usage (all time) (usegalaxy.org.au): 230 + Tool usage (all time) - all main servers: 2478 + ToolShed categories: + - Fasta Manipulation + - Proteomics + ToolShed id: filter_by_fasta_ids + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: flashlfq + Conda version: 1.2.6 + Date of first commit of the suite: '2017-12-06' + Description: FlashLFQ mass-spectrometry proteomics label-free quantification + EDAM operation: + - Label-free quantification + EDAM operation (no superclasses): + - Label-free quantification + EDAM topic: + - Proteomics experiment + - Proteomics + EDAM topic (no superclasses): + - Proteomics experiment + - Proteomics + Galaxy tool ids: + - flashlfq + Galaxy wrapper id: flashlfq + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq + Galaxy wrapper version: 1.0.3.1 + No. of tool users (5 years) (usegalaxy.eu): 661 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 167 + No. of tool users (5 years) - all main servers: 828 + No. of tool users (all time) (usegalaxy.eu): 715 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 167 + No. of tool users (all time) - all main servers: 882 + Source: https://github.com/smith-chem-wisc/FlashLFQ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 52 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 15 + Tool usage (5 years) - all main servers: 67 + Tool usage (all time) (usegalaxy.eu): 54 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 15 + Tool usage (all time) - all main servers: 69 + ToolShed categories: + - Proteomics + ToolShed id: flashlfq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: FlashLFQ is an ultrafast label-free quantification algorithm + for mass-spectrometry proteomics. + bio.tool id: flashlfq + bio.tool ids: + - flashlfq + bio.tool name: FlashLFQ +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: fragpipe + Conda version: '20.0' + Date of first commit of the suite: '2023-05-10' + Description: Data analysis for mass spectrometry-based proteomics. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - fragpipe + Galaxy wrapper id: fragpipe + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe + Galaxy wrapper version: '20.0' + No. of tool users (5 years) (usegalaxy.eu): 64 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 64 + No. of tool users (all time) (usegalaxy.eu): 64 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 64 + Source: https://fragpipe.nesvilab.org/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Proteomics + ToolShed id: fragpipe + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2018-01-10' + Description: Filter and convert a gffCompare GTF to BED + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gffcompare_to_bed + Galaxy wrapper id: gffcompare_to_bed + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed + Galaxy wrapper version: 0.2.1 + No. of tool users (5 years) (usegalaxy.eu): 1375 + No. of tool users (5 years) (usegalaxy.org): 1071 + No. of tool users (5 years) (usegalaxy.org.au): 492 + No. of tool users (5 years) - all main servers: 2938 + No. of tool users (all time) (usegalaxy.eu): 2230 + No. of tool users (all time) (usegalaxy.org): 1071 + No. of tool users (all time) (usegalaxy.org.au): 492 + No. of tool users (all time) - all main servers: 3793 + Source: https://github.com/gpertea/gffcompare/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 329 + Tool usage (5 years) (usegalaxy.org): 362 + Tool usage (5 years) (usegalaxy.org.au): 64 + Tool usage (5 years) - 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It is specifically aimed at high-resolution + MS data. + bio.tool id: maxquant + bio.tool ids: + - maxquant + bio.tool name: MaxQuant +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mpa-portable + Conda version: 2.0.0 + Date of first commit of the suite: '2017-03-03' + Description: MetaProteomeAnalyzer + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - meta_proteome_analyzer + Galaxy wrapper id: meta_proteome_analyzer + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer + Galaxy wrapper version: 2.0.0 + No. of tool users (5 years) (usegalaxy.eu): 126 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 126 + No. of tool users (all time) (usegalaxy.eu): 126 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 126 + Source: https://github.com/compomics/meta-proteome-analyzer/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 20 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 20 + ToolShed categories: + - Proteomics + ToolShed id: meta_proteome_analyzer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: metagene_annotator + Conda version: '1.0' + Date of first commit of the suite: '2018-03-21' + Description: MetaGeneAnnotator gene-finding program for prokaryote and phage + EDAM operation: + - Sequence annotation + EDAM operation (no superclasses): + - Sequence annotation + EDAM topic: + - Genomics + - Model organisms + - Data submission, annotation and curation + EDAM topic (no superclasses): + - Genomics + - Model organisms + - Data submission, annotation and curation + Galaxy tool ids: + - metagene_annotator + Galaxy wrapper id: metagene_annotator + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 980 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 980 + No. of tool users (all time) (usegalaxy.eu): 980 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 980 + Source: http://metagene.nig.ac.jp/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 323 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 323 + Tool usage (all time) (usegalaxy.eu): 323 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 323 + ToolShed categories: + - Sequence Analysis + ToolShed id: metagene_annotator + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: Prokaryotic gene finding program from environmental genome + shotgun sequences or metagenomic sequences. + bio.tool id: metageneannotator + bio.tool ids: + - metageneannotator + bio.tool name: MetaGeneAnnotator +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: metanovo + Conda version: 1.9.4 + Date of first commit of the suite: '2022-03-29' + Description: Produce targeted databases for mass spectrometry analysis. + EDAM operation: + - Target-Decoy + - de Novo sequencing + - Tag-based peptide identification + - Protein identification + - Expression analysis + EDAM operation (no superclasses): + - Target-Decoy + - de Novo sequencing + - Tag-based peptide identification + - Protein identification + - Expression analysis + EDAM topic: + - Proteomics + - Microbial ecology + - Metagenomics + - Proteomics experiment + - Small molecules + EDAM topic (no superclasses): + - Proteomics + - Microbial ecology + - Metagenomics + - Proteomics experiment + - Small molecules + Galaxy tool ids: + - metanovo + Galaxy wrapper id: metanovo + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo + Galaxy wrapper version: 1.9.4 + No. of tool users (5 years) (usegalaxy.eu): 4471 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4471 + No. of tool users (all time) (usegalaxy.eu): 4471 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4471 + Source: https://github.com/uct-cbio/proteomics-pipelines + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 29 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 29 + Tool usage (all time) (usegalaxy.eu): 29 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 29 + ToolShed categories: + - Proteomics + ToolShed id: metanovo + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: An open-source pipeline for probabilistic peptide discovery + in complex metaproteomic datasets. + bio.tool id: metanovo + bio.tool ids: + - metanovo + bio.tool name: MetaNovo +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 6 + Conda id: metaquantome + Conda version: 2.0.2 + Date of first commit of the suite: '2019-04-05' + Description: quantitative analysis of microbiome taxonomy and function + EDAM operation: + - Principal component visualisation + - Visualisation + - Functional clustering + - Query and retrieval + - Differential protein expression analysis + - Heat map generation + - Quantification + - Indexing + - Filtering + - Statistical inference + EDAM operation (no superclasses): + - Principal component visualisation + - Functional clustering + - Query and retrieval + - Heat map generation + - Quantification + - Indexing + - Filtering + - Statistical inference + EDAM topic: + - Proteomics + - Metatranscriptomics + - Microbial ecology + - Proteomics experiment + - Metagenomics + EDAM topic (no superclasses): + - Proteomics + - Metatranscriptomics + - Microbial ecology + - Proteomics experiment + - Metagenomics + Galaxy tool ids: + - metaquantome_db + - metaquantome_expand + - metaquantome_filter + - metaquantome_sample + - metaquantome_stat + - metaquantome_viz + Galaxy wrapper id: metaquantome + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome + Galaxy wrapper version: 2.0.2 + No. of tool users (5 years) (usegalaxy.eu): 2730 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 1540 + No. of tool users (5 years) - all main servers: 4270 + No. of tool users (all time) (usegalaxy.eu): 2831 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 1540 + No. of tool users (all time) - all main servers: 4371 + Source: https://github.com/galaxyproteomics/metaquantome/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 260 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 71 + Tool usage (5 years) - all main servers: 331 + Tool usage (all time) (usegalaxy.eu): 262 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 71 + Tool usage (all time) - all main servers: 333 + ToolShed categories: + - Proteomics + ToolShed id: metaquantome + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 6 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 6 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 6 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 6 + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.no: 6 + UseGalaxy.or: 6 + biii: null + bio.tool description: metaQuantome software suite analyzes the state of a microbiome + by leveraging complex taxonomic and functional hierarchies to summarize peptide-level + quantitative information. metaQuantome offers differential abundance analysis, + principal components analysis, and clustered heat map visualizations, as well + as exploratory analysis for a single sample or experimental condition. + bio.tool id: metaQuantome + bio.tool ids: + - metaQuantome + bio.tool name: metaQuantome +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: mgf-formatter + Conda version: 1.0.0 + Date of first commit of the suite: '2014-09-26' + Description: null + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mgf_formatter + Galaxy wrapper id: mgf_formatter + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter + Galaxy wrapper source: null + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: [] + ToolShed id: mgf_formatter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: moff + Conda version: 2.0.3 + Date of first commit of the suite: '2019-01-28' + Description: moFF (a modest Feature Finder) extracts MS1 intensities from RAW and + mzML spectrum files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomics_moff + Galaxy wrapper id: moFF + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF + Galaxy wrapper version: 2.0.3 + No. of tool users (5 years) (usegalaxy.eu): 331 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 137 + No. of tool users (5 years) - all main servers: 468 + No. of tool users (all time) (usegalaxy.eu): 762 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 137 + No. of tool users (all time) - all main servers: 899 + Source: https://github.com/compomics/moFF + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 24 + Tool usage (all time) (usegalaxy.eu): 34 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 38 + ToolShed categories: + - Proteomics + ToolShed id: proteomics_moff + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: morpheus + Conda version: '290' + Date of first commit of the suite: '2015-10-29' + Description: Morpheus MS Search Application + EDAM operation: + - Peptide database search + EDAM operation (no superclasses): + - Peptide database search + EDAM topic: + - Proteomics + EDAM topic (no superclasses): + - Proteomics + Galaxy tool ids: + - morpheus + Galaxy wrapper id: morpheus + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus + Galaxy wrapper version: '288' + No. of tool users (5 years) (usegalaxy.eu): 105 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 833 + No. of tool users (5 years) - all main servers: 938 + No. of tool users (all time) (usegalaxy.eu): 153 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 833 + No. of tool users (all time) - all main servers: 986 + Source: https://cwenger.github.io/Morpheus + Status: To update + Tool usage (5 years) (usegalaxy.eu): 12 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 93 + Tool usage (5 years) - all main servers: 105 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 93 + Tool usage (all time) - all main servers: 112 + ToolShed categories: + - Proteomics + ToolShed id: morpheus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: A proteomics search algorithm specifically designed for high-resolution + tandem mass spectra. + bio.tool id: morpheus + bio.tool ids: + - morpheus + bio.tool name: Morpheus +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-preprocesscore + Conda version: 1.64.0 + Date of first commit of the suite: '2022-03-31' + Description: MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mqppep_anova + - mqppep_preproc + Galaxy wrapper id: mqppep + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep + Galaxy wrapper version: 0.1.19 + No. of tool users (5 years) (usegalaxy.eu): 13 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 13 + No. of tool users (all time) (usegalaxy.eu): 13 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 13 + Source: https://github.com/galaxyproteomics/tools-galaxyp/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 3 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Proteomics + ToolShed id: mqppep + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2019-02-14' + Description: msconvert Convert and/or filter mass spectrometry files (including + vendor formats) using the official Docker container + EDAM operation: + - Filtering + - Formatting + EDAM operation (no superclasses): + - Filtering + - Formatting + EDAM topic: + - Proteomics + - Proteomics experiment + EDAM topic (no superclasses): + - Proteomics + - Proteomics experiment + Galaxy tool ids: + - msconvert + Galaxy wrapper id: msconvert + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert + Galaxy wrapper version: 3.0.20287 + No. of tool users (5 years) (usegalaxy.eu): 20749 + No. of tool users (5 years) (usegalaxy.org): 1239 + No. of tool users (5 years) (usegalaxy.org.au): 2666 + No. of tool users (5 years) - all main servers: 24654 + No. of tool users (all time) (usegalaxy.eu): 22184 + No. of tool users (all time) (usegalaxy.org): 1239 + No. of tool users (all time) (usegalaxy.org.au): 2666 + No. of tool users (all time) - all main servers: 26089 + Source: http://proteowizard.sourceforge.net/tools.shtml + Status: To update + Tool usage (5 years) (usegalaxy.eu): 455 + Tool usage (5 years) (usegalaxy.org): 71 + Tool usage (5 years) (usegalaxy.org.au): 53 + Tool usage (5 years) - all main servers: 579 + Tool usage (all time) (usegalaxy.eu): 469 + Tool usage (all time) (usegalaxy.org): 71 + Tool usage (all time) (usegalaxy.org.au): 53 + Tool usage (all time) - all main servers: 593 + ToolShed categories: + - Proteomics + ToolShed id: msconvert + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: msConvert is a command-line utility for converting between + various mass spectrometry data formats, including from raw data from several commercial + companies (with vendor libraries, Windows-only). For Windows users, there is also + a GUI, msConvertGUI. + bio.tool id: msconvert + bio.tool ids: + - msconvert + bio.tool name: msConvert +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: msgf_plus + Conda version: 2024.03.26 + Date of first commit of the suite: '2017-01-12' + Description: MSGF+ + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - msgfplus + Galaxy wrapper id: msgfplus + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus + Galaxy wrapper version: '0.5' + No. of tool users (5 years) (usegalaxy.eu): 473 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 473 + No. of tool users (all time) (usegalaxy.eu): 529 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 529 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 33 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 33 + Tool usage (all time) (usegalaxy.eu): 43 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 43 + ToolShed categories: + - Proteomics + ToolShed id: msgfplus + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteowizard + Conda version: '3_0_9992' + Date of first commit of the suite: '2019-10-23' + Description: Extract MS/MS scans from the mzML file(s) based on PSM report. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - msms_extractor + Galaxy wrapper id: msms_extractor + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor + Galaxy wrapper source: null + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 110 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 110 + No. of tool users (all time) (usegalaxy.eu): 110 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 110 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Proteomics + ToolShed id: msms_extractor + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-msstats + Conda version: 4.10.0 + Date of first commit of the suite: '2020-07-25' + Description: MSstats tool for analyzing mass spectrometry proteomic datasets + EDAM operation: + - Spectrum calculation + - Tag-based peptide identification + - Differential protein expression profiling + EDAM operation (no superclasses): + - Spectrum calculation + - Tag-based peptide identification + - Differential protein expression profiling + EDAM topic: + - Proteomics + - Proteomics experiment + - Protein expression + EDAM topic (no superclasses): + - Proteomics + - Proteomics experiment + - Protein expression + Galaxy tool ids: + - msstats + Galaxy wrapper id: msstats + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats + Galaxy wrapper version: 4.0.0 + No. of tool users (5 years) (usegalaxy.eu): 2353 + No. of tool users (5 years) (usegalaxy.org): 1122 + No. of tool users (5 years) (usegalaxy.org.au): 1091 + No. of tool users (5 years) - all main servers: 4566 + No. of tool users (all time) (usegalaxy.eu): 2353 + No. of tool users (all time) (usegalaxy.org): 1122 + No. of tool users (all time) (usegalaxy.org.au): 1091 + No. of tool users (all time) - all main servers: 4566 + Source: https://github.com/MeenaChoi/MSstats + Status: To update + Tool usage (5 years) (usegalaxy.eu): 559 + Tool usage (5 years) (usegalaxy.org): 211 + Tool usage (5 years) (usegalaxy.org.au): 35 + Tool usage (5 years) - all main servers: 805 + Tool usage (all time) (usegalaxy.eu): 559 + Tool usage (all time) (usegalaxy.org): 211 + Tool usage (all time) (usegalaxy.org.au): 35 + Tool usage (all time) - all main servers: 805 + ToolShed categories: + - Proteomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Tools for detecting differentially abundant peptides and proteins + in shotgun mass spectrometry-based proteomic experiments with tandem mass tag + (TMT) labeling + bio.tool id: msstatstmt + bio.tool ids: + - msstatstmt + bio.tool name: MSstatsTMT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-msstatstmt + Conda version: 2.10.0 + Date of first commit of the suite: '2021-02-26' + Description: MSstatsTMT protein significance analysis in shotgun mass spectrometry-based + proteomic experiments with tandem mass tag (TMT) labeling + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - msstatstmt + Galaxy wrapper id: msstatstmt + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt + Galaxy wrapper version: 2.0.0 + No. of tool users (5 years) (usegalaxy.eu): 795 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 461 + No. of tool users (5 years) - all main servers: 1256 + No. of tool users (all time) (usegalaxy.eu): 795 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 461 + No. of tool users (all time) - all main servers: 1256 + Source: http://msstats.org/msstatstmt/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 104 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 12 + Tool usage (5 years) - all main servers: 116 + Tool usage (all time) (usegalaxy.eu): 104 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 12 + Tool usage (all time) - all main servers: 116 + ToolShed categories: + - Proteomics + ToolShed id: msstatstmt + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-tidyverse + Conda version: null + Date of first commit of the suite: '2020-06-23' + Description: Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mt2mq + Galaxy wrapper id: mt2mq + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq + Galaxy wrapper source: null + Galaxy wrapper version: 1.1.0 + No. of tool users (5 years) (usegalaxy.eu): 275 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 275 + No. of tool users (all time) (usegalaxy.eu): 275 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 275 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 38 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 38 + Tool usage (all time) (usegalaxy.eu): 38 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 38 + ToolShed categories: + - Proteomics + ToolShed id: mt2mq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: mztosqlite + Conda version: 2.1.1 + Date of first commit of the suite: '2015-06-01' + Description: Creates a SQLite database for proteomics data + EDAM operation: + - Conversion + - Peptide database search + EDAM operation (no superclasses): + - Conversion + - Peptide database search + EDAM topic: + - Proteomics + - Biological databases + EDAM topic (no superclasses): + - Proteomics + - Biological databases + Galaxy tool ids: + - mz_to_sqlite + Galaxy wrapper id: mz_to_sqlite + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite + Galaxy wrapper version: 2.1.1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 854 + No. of tool users (5 years) (usegalaxy.org): 79 + No. of tool users (5 years) (usegalaxy.org.au): 274 + No. of tool users (5 years) - all main servers: 1207 + No. of tool users (all time) (usegalaxy.eu): 860 + No. of tool users (all time) (usegalaxy.org): 79 + No. of tool users (all time) (usegalaxy.org.au): 274 + No. of tool users (all time) - all main servers: 1213 + Source: https://github.com/galaxyproteomics/mzToSQLite + Status: To update + Tool usage (5 years) (usegalaxy.eu): 110 + Tool usage (5 years) (usegalaxy.org): 15 + Tool usage (5 years) (usegalaxy.org.au): 13 + Tool usage (5 years) - all main servers: 138 + Tool usage (all time) (usegalaxy.eu): 111 + Tool usage (all time) (usegalaxy.org): 15 + Tool usage (all time) (usegalaxy.org.au): 13 + Tool usage (all time) - all main servers: 139 + ToolShed categories: + - Proteomics + ToolShed id: mz_to_sqlite + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Convert proteomics data files into a SQLite database + bio.tool id: mztosqlite + bio.tool ids: + - mztosqlite + bio.tool name: mzToSQLite +- Available on UseGalaxy.eu: 144 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 8 + Available on UseGalaxy.org.au: 34 + Conda id: openms + Conda version: 3.2.0 + Date of first commit of the suite: '2024-04-09' + Description: OpenMS Suite for LC/MS data management and analyses + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - AccurateMassSearch + - AssayGeneratorMetabo + - BaselineFilter + - CVInspector + - ClusterMassTraces + - ClusterMassTracesByPrecursor + - CometAdapter + - ConsensusID + - ConsensusMapNormalizer + - DTAExtractor + - DatabaseFilter + - DatabaseSuitability + - DeMeanderize + - DecoyDatabase + - Digestor + - DigestorMotif + - EICExtractor + - ERPairFinder + - Epifany + - ExternalCalibration + - FalseDiscoveryRate + - FeatureFinderCentroided + - FeatureFinderIdentification + - FeatureFinderIsotopeWavelet + - FeatureFinderMRM + - FeatureFinderMetabo + - FeatureFinderMetaboIdent + - FeatureFinderMultiplex + - FeatureLinkerLabeled + - FeatureLinkerUnlabeled + - FeatureLinkerUnlabeledKD + - FeatureLinkerUnlabeledQT + - FileConverter + - FileFilter + - FileInfo + - FileMerger + - FuzzyDiff + - GNPSExport + - HighResPrecursorMassCorrector + - IDConflictResolver + - IDExtractor + - IDFileConverter + - IDFilter + - IDMapper + - IDMassAccuracy + - IDMerger + - IDPosteriorErrorProbability + - IDRTCalibration + - IDRipper + - IDScoreSwitcher + - IDSplitter + - InternalCalibration + - IsobaricAnalyzer + - JSONExporter + - LuciphorAdapter + - MRMMapper + - MRMPairFinder + - MRMTransitionGroupPicker + - MSFraggerAdapter + - MSGFPlusAdapter + - MSstatsConverter + - MapAlignerIdentification + - MapAlignerPoseClustering + - MapAlignerSpectrum + - MapAlignerTreeGuided + - MapNormalizer + - MapRTTransformer + - MapStatistics + - MascotAdapter + - MascotAdapterOnline + - MassCalculator + - MassTraceExtractor + - MetaProSIP + - MetaboliteSpectralMatcher + - MultiplexResolver + - MzMLSplitter + - MzTabExporter + - NoiseFilterGaussian + - NoiseFilterSGolay + - NovorAdapter + - NucleicAcidSearchEngine + - OpenMSDatabasesInfo + - OpenMSInfo + - OpenPepXL + - OpenPepXLLF + - OpenSwathAnalyzer + - OpenSwathAssayGenerator + - OpenSwathChromatogramExtractor + - OpenSwathConfidenceScoring + - OpenSwathDIAPreScoring + - OpenSwathDecoyGenerator + - OpenSwathFeatureXMLToTSV + - OpenSwathFileSplitter + - OpenSwathMzMLFileCacher + - OpenSwathRTNormalizer + - OpenSwathRewriteToFeatureXML + - OpenSwathWorkflow + - PSMFeatureExtractor + - PeakPickerHiRes + - PeakPickerIterative + - PeakPickerWavelet + - PeptideIndexer + - PercolatorAdapter + - PhosphoScoring + - PrecursorMassCorrector + - ProteinInference + - ProteinQuantifier + - ProteinResolver + - QCCalculator + - QCEmbedder + - QCExporter + - QCExtractor + - QCImporter + - QCMerger + - QCShrinker + - QualityControl + - RNADigestor + - RNAMassCalculator + - RNPxlSearch + - RNPxlXICFilter + - SageAdapter + - SeedListGenerator + - SemanticValidator + - SequenceCoverageCalculator + - SimpleSearchEngine + - SiriusAdapter + - SpecLibCreator + - SpecLibSearcher + - SpectraFilterBernNorm + - SpectraFilterMarkerMower + - SpectraFilterNLargest + - SpectraFilterNormalizer + - SpectraFilterParentPeakMower + - SpectraFilterScaler + - SpectraFilterSqrtMower + - SpectraFilterThresholdMower + - SpectraFilterWindowMower + - SpectraMerger + - SpectraSTSearchAdapter + - StaticModification + - TICCalculator + - TOFCalibration + - TargetedFileConverter + - TextExporter + - TriqlerConverter + - XFDR + - XMLValidator + - XTandemAdapter + Galaxy wrapper id: openms + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms + Galaxy wrapper version: '3.1' + No. of tool users (5 years) (usegalaxy.eu): 32169 + No. of tool users (5 years) (usegalaxy.org): 50 + No. of tool users (5 years) (usegalaxy.org.au): 940 + No. of tool users (5 years) - all main servers: 33159 + No. of tool users (all time) (usegalaxy.eu): 108654 + No. of tool users (all time) (usegalaxy.org): 50 + No. of tool users (all time) (usegalaxy.org.au): 940 + No. of tool users (all time) - all main servers: 109644 + Source: https://www.openms.de/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3316 + Tool usage (5 years) (usegalaxy.org): 15 + Tool usage (5 years) (usegalaxy.org.au): 245 + Tool usage (5 years) - all main servers: 3576 + Tool usage (all time) (usegalaxy.eu): 4889 + Tool usage (all time) (usegalaxy.org): 15 + Tool usage (all time) (usegalaxy.org.au): 245 + Tool usage (all time) - all main servers: 5149 + ToolShed categories: + - Proteomics + ToolShed id: openms + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 18 + Tools available on UseGalaxy.cz: 141 + Tools available on UseGalaxy.eu: 144 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 124 + Tools available on UseGalaxy.org (Main): 8 + Tools available on UseGalaxy.org.au: 34 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 18 + UseGalaxy.cz: 141 + UseGalaxy.eu: 144 + UseGalaxy.no: 124 + UseGalaxy.or: 34 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pathwaymatcher + Conda version: 1.9.1 + Date of first commit of the suite: '2018-06-08' + Description: Reactome Pathway Matcher + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - reactome_pathwaymatcher + Galaxy wrapper id: pathwaymatcher + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher + Galaxy wrapper version: null + No. of tool users (5 years) (usegalaxy.eu): 174 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 174 + No. of tool users (all time) (usegalaxy.eu): 244 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 244 + Source: https://github.com/LuisFranciscoHS/PathwayMatcher + Status: To update + Tool usage (5 years) (usegalaxy.eu): 65 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 65 + Tool usage (all time) (usegalaxy.eu): 76 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 76 + ToolShed categories: + - Proteomics + ToolShed id: reactome_pathwaymatcher + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2017-12-19' + Description: PepPointer categorizes peptides by their genomic coordinates. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pep_pointer + Galaxy wrapper id: pep_pointer + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer + Galaxy wrapper version: 0.1.3+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 506 + No. of tool users (5 years) (usegalaxy.org): 21 + No. of tool users (5 years) (usegalaxy.org.au): 163 + No. of tool users (5 years) - all main servers: 690 + No. of tool users (all time) (usegalaxy.eu): 511 + No. of tool users (all time) (usegalaxy.org): 21 + No. of tool users (all time) (usegalaxy.org.au): 163 + No. of tool users (all time) - all main servers: 695 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 54 + Tool usage (5 years) (usegalaxy.org): 12 + Tool usage (5 years) (usegalaxy.org.au): 8 + Tool usage (5 years) - all main servers: 74 + Tool usage (all time) (usegalaxy.eu): 55 + Tool usage (all time) (usegalaxy.org): 12 + Tool usage (all time) (usegalaxy.org.au): 8 + Tool usage (all time) - all main servers: 75 + ToolShed categories: + - Genomic Interval Operations + - Proteomics + ToolShed id: pep_pointer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pepquery + Conda version: 2.0.2 + Date of first commit of the suite: '2020-01-22' + Description: A peptide-centric MS search engine for novel peptide identification + and validation. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pepquery + Galaxy wrapper id: pepquery + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery + Galaxy wrapper version: 1.6.2 + No. of tool users (5 years) (usegalaxy.eu): 7047 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 7047 + No. of tool users (all time) (usegalaxy.eu): 7047 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 7047 + Source: https://pepquery.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 76 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 76 + Tool usage (all time) (usegalaxy.eu): 76 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 76 + ToolShed categories: + - Proteomics + ToolShed id: pepquery + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: pepquery + Conda version: 2.0.2 + Date of first commit of the suite: '2022-10-02' + Description: PepQuery2 peptide-centric MS search for peptide identification and + validation + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pepquery2 + - pepquery2_index + - pepquery2_show_sets + Galaxy wrapper id: pepquery2 + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 + Galaxy wrapper version: 2.0.2 + No. of tool users (5 years) (usegalaxy.eu): 1222 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1222 + No. of tool users (all time) (usegalaxy.eu): 1222 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1222 + Source: https://pepquery.org + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 28 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 28 + Tool usage (all time) (usegalaxy.eu): 28 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 28 + ToolShed categories: + - Proteomics + ToolShed id: pepquery2 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-03-29' + Description: Gets genomic coordinate of peptides based on the information in mzsqlite + and genomic mapping sqlite files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - peptide_genomic_coordinate + Galaxy wrapper id: peptide_genomic_coordinate + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate + Galaxy wrapper source: null + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 472 + No. of tool users (5 years) (usegalaxy.org): 16 + No. of tool users (5 years) (usegalaxy.org.au): 149 + No. of tool users (5 years) - all main servers: 637 + No. of tool users (all time) (usegalaxy.eu): 472 + No. of tool users (all time) (usegalaxy.org): 16 + No. of tool users (all time) (usegalaxy.org.au): 149 + No. of tool users (all time) - all main servers: 637 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 56 + Tool usage (5 years) (usegalaxy.org): 10 + Tool usage (5 years) (usegalaxy.org.au): 5 + Tool usage (5 years) - all main servers: 71 + Tool usage (all time) (usegalaxy.eu): 56 + Tool usage (all time) (usegalaxy.org): 10 + Tool usage (all time) (usegalaxy.org.au): 5 + Tool usage (all time) - 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translate_bed + Galaxy wrapper id: translate_bed + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 649 + No. of tool users (5 years) (usegalaxy.org): 473 + No. of tool users (5 years) (usegalaxy.org.au): 761 + No. of tool users (5 years) - all main servers: 1883 + No. of tool users (all time) (usegalaxy.eu): 685 + No. of tool users (all time) (usegalaxy.org): 473 + No. of tool users (all time) (usegalaxy.org.au): 761 + No. of tool users (all time) - all main servers: 1919 + Source: http://rest.ensembl.org/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 138 + Tool usage (5 years) (usegalaxy.org): 105 + Tool usage (5 years) (usegalaxy.org.au): 18 + Tool usage (5 years) - all main servers: 261 + Tool usage (all time) (usegalaxy.eu): 142 + Tool usage (all time) (usegalaxy.org): 105 + Tool usage (all time) (usegalaxy.org.au): 18 + Tool usage (all time) - all main servers: 265 + ToolShed categories: + - Proteomics + ToolShed id: translate_bed + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-joinquantpepionswithproteins + Conda version: 0.0.2 + Date of first commit of the suite: '2021-09-16' + Description: The tool JoinQuantPepIonsWithProteins combines results from ProteinInference + and PSMBasedQuantification. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_joinquantpepionswithproteins + Galaxy wrapper id: proteomiqon_joinquantpepionswithproteins + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 366 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 366 + No. of tool users (all time) (usegalaxy.eu): 366 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 366 + Source: https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_joinquantpepionswithproteins + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-labeledproteinquantification + Conda version: 0.0.3 + Date of first commit of the suite: '2021-09-16' + Description: The tool LabeledProteinQuantification estimates protein abundances + using quantified peptide ions. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_labeledproteinquantification + Galaxy wrapper id: proteomiqon_labeledproteinquantification + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 16 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 16 + No. of tool users (all time) (usegalaxy.eu): 16 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 16 + Source: https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_labeledproteinquantification + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-labelfreeproteinquantification + Conda version: 0.0.3 + Date of first commit of the suite: '2021-10-13' + Description: The tool LabelFreeProteinQuantification estimates protein abundances + using quantified peptide ions. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_labelfreeproteinquantification + Galaxy wrapper id: proteomiqon_labelfreeproteinquantification + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 6 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6 + No. of tool users (all time) (usegalaxy.eu): 6 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6 + Source: https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_labelfreeproteinquantification + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-mzmltomzlite + Conda version: 0.0.8 + Date of first commit of the suite: '2021-06-30' + Description: The tool MzMLToMzLite allows to convert mzML files to mzLite files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_mzmltomzlite + Galaxy wrapper id: proteomiqon_mzmltomzlite + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite + Galaxy wrapper version: 0.0.8 + No. of tool users (5 years) (usegalaxy.eu): 721 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 721 + No. of tool users (all time) (usegalaxy.eu): 721 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 721 + Source: https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_mzmltomzlite + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-peptidedb + Conda version: 0.0.7 + Date of first commit of the suite: '2021-07-04' + Description: The tool ProteomIQon PeptideDB creates a peptide database in the SQLite + format. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_peptidedb + Galaxy wrapper id: proteomiqon_peptidedb + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb + Galaxy wrapper version: 0.0.7 + No. of tool users (5 years) (usegalaxy.eu): 96 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 96 + No. of tool users (all time) (usegalaxy.eu): 96 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 96 + Source: https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 12 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 12 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 12 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_peptidedb + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-peptidespectrummatching + Conda version: 0.0.7 + Date of first commit of the suite: '2021-07-15' + Description: Given raw an MS run in the mzLite format, this tool iterates across + all MS/MS scans, determines precursor charge states and possible peptide spectrum + matches using reimplementations of SEQUEST,Andromeda and XTandem. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_peptidespectrummatching + Galaxy wrapper id: proteomiqon_peptidespectrummatching + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching + Galaxy wrapper version: 0.0.7 + No. of tool users (5 years) (usegalaxy.eu): 686 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 686 + No. of tool users (all time) (usegalaxy.eu): 686 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 686 + Source: https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_peptidespectrummatching + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-proteininference + Conda version: 0.0.7 + Date of first commit of the suite: '2021-07-09' + Description: 'MS-based shotgun proteomics estimates protein abundances using a proxy: + peptides. The process of ''Protein Inference'' is concerned with the mapping of + identified peptides to the proteins they putatively originated from.' + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_proteininference + Galaxy wrapper id: proteomiqon_proteininference + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference + Galaxy wrapper version: 0.0.7 + No. of tool users (5 years) (usegalaxy.eu): 89 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 89 + No. of tool users (all time) (usegalaxy.eu): 89 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 89 + Source: https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_proteininference + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-psmbasedquantification + Conda version: 0.0.9 + Date of first commit of the suite: '2021-07-09' + Description: The PSMBasedQuantification tool was designed to allow label-free quantification + as well as quantification of full metabolic labeled samples. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_psmbasedquantification + Galaxy wrapper id: proteomiqon_psmbasedquantification + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification + Galaxy wrapper version: 0.0.8 + No. of tool users (5 years) (usegalaxy.eu): 604 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 604 + No. of tool users (all time) (usegalaxy.eu): 604 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 604 + Source: https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_psmbasedquantification + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: proteomiqon-psmstatistics + Conda version: 0.0.8 + Date of first commit of the suite: '2021-07-09' + Description: The PSMStatistics tool utilizes semi supervised machine learning techniques + to integrate search engine scores as well as the mentioned quality scores into + one single consensus score. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteomiqon_psmstatistics + Galaxy wrapper id: proteomiqon_psmstatistics + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics + Galaxy wrapper version: 0.0.8 + No. of tool users (5 years) (usegalaxy.eu): 694 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 694 + No. of tool users (all time) (usegalaxy.eu): 694 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 694 + Source: https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Proteomics + ToolShed id: proteomiqon_psmstatistics + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2021-05-17' + Description: ProteoRE JVenn Diagram + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - proteore_venn_diagram + Galaxy wrapper id: proteore_venn_diagram + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram + Galaxy wrapper source: null + Galaxy wrapper version: 2021.06.08 + No. of tool users (5 years) (usegalaxy.eu): 15 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 15 + No. of tool users (all time) (usegalaxy.eu): 15 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 15 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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all main servers: 21 + ToolShed categories: + - Proteomics + ToolShed id: translate_bed_sequences + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2015-04-03' + Description: Unipept retrieves metaproteomics information + EDAM operation: + - Prediction and recognition + - Visualisation + EDAM operation (no superclasses): + - Prediction and recognition + - Visualisation + EDAM topic: + - Proteomics + - Proteogenomics + - Biodiversity + - Workflows + EDAM topic (no superclasses): + - Proteomics + - Proteogenomics + - Biodiversity + - Workflows + Galaxy tool ids: + - unipept + Galaxy wrapper id: unipept + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept + Galaxy wrapper source: https://unipept.ugent.be/apidocs + Galaxy wrapper version: 4.5.1 + No. of tool users (5 years) (usegalaxy.eu): 4900 + No. of tool users (5 years) (usegalaxy.org): 251 + No. of tool users (5 years) (usegalaxy.org.au): 1069 + No. of tool users (5 years) - all main servers: 6220 + No. of tool users (all time) (usegalaxy.eu): 5146 + No. of tool users (all time) (usegalaxy.org): 251 + No. of tool users (all time) (usegalaxy.org.au): 1069 + No. of tool users (all time) - all main servers: 6466 + Source: https://github.com/galaxyproteomics/tools-galaxyp + Status: To update + Tool usage (5 years) (usegalaxy.eu): 257 + Tool usage (5 years) (usegalaxy.org): 81 + Tool usage (5 years) (usegalaxy.org.au): 29 + Tool usage (5 years) - all main servers: 367 + Tool usage (all time) (usegalaxy.eu): 270 + Tool usage (all time) (usegalaxy.org): 81 + Tool usage (all time) (usegalaxy.org.au): 29 + Tool usage (all time) - all main servers: 380 + ToolShed categories: + - Proteomics + ToolShed id: unipept + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 1 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Metaproteomics data analysis with a focus on interactive data + visualizations. + bio.tool id: unipept + bio.tool ids: + - unipept + bio.tool name: Unipept +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: requests + Conda version: null + Date of first commit of the suite: '2016-03-08' + Description: Download UniProt proteome in XML or fasta format + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - uniprotxml_downloader + Galaxy wrapper id: uniprotxml_downloader + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader + Galaxy wrapper version: 2.4.0 + No. of tool users (5 years) (usegalaxy.eu): 1488 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 743 + No. of tool users (5 years) - all main servers: 2231 + No. of tool users (all time) (usegalaxy.eu): 1596 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 743 + No. of tool users (all time) - all main servers: 2339 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 230 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 35 + Tool usage (5 years) - all main servers: 265 + Tool usage (all time) (usegalaxy.eu): 266 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 35 + Tool usage (all time) - all main servers: 301 + ToolShed categories: + - Proteomics + ToolShed id: uniprotxml_downloader + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: validate-fasta-database + Conda version: '1.0' + Date of first commit of the suite: '2017-09-14' + Description: runs Compomics database identification tool on any FASTA database, + and separates valid and invalid entries based on a series of checks. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - validate_fasta_database + Galaxy wrapper id: validate_fasta_database + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database + Galaxy wrapper source: null + Galaxy wrapper version: 0.1.5 + No. of tool users (5 years) (usegalaxy.eu): 112 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 112 + No. of tool users (all time) (usegalaxy.eu): 112 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 112 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 38 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 38 + Tool usage (all time) (usegalaxy.eu): 38 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 38 + ToolShed categories: + - Fasta Manipulation + - Proteomics + ToolShed id: validate_fasta_database + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: shapely + Conda version: null + Date of first commit of the suite: '2024-06-29' + Description: Converts coordinates from a tabular file into a formatted text file + readable by Zeiss laser-capture microdissection systems + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ZeissLMDconverter + Galaxy wrapper id: zeiss_lmd_converter + Galaxy wrapper owner: galaxyp + Galaxy wrapper parsed folder: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter + Galaxy wrapper source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter + Galaxy wrapper version: 2.0.4 + No. of tool users (5 years) (usegalaxy.eu): 4 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 4 + No. of tool users (all time) (usegalaxy.eu): 4 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 4 + Source: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Proteomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 4 + Conda id: r-bio3d + Conda version: '2.3_3' + Date of first commit of the suite: '2018-10-03' + Description: Bio3d is a program that can be used to analyse molecular dynamics trajectories. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - bio3d_dccm + - bio3d_pca + - bio3d_rmsd + - bio3d_rmsf + - bio3d_pca_visualize + Galaxy wrapper id: bio3d + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d + Galaxy wrapper version: '2.4_1' + No. of tool users (5 years) (usegalaxy.eu): 10600 + No. of tool users (5 years) (usegalaxy.org): 1042 + No. of tool users (5 years) (usegalaxy.org.au): 2756 + No. of tool users (5 years) - all main servers: 14398 + No. of tool users (all time) (usegalaxy.eu): 10729 + No. of tool users (all time) (usegalaxy.org): 1042 + No. of tool users (all time) (usegalaxy.org.au): 2756 + No. of tool users (all time) - all main servers: 14527 + Source: http://thegrantlab.org/bio3d/index.php + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1150 + Tool usage (5 years) (usegalaxy.org): 255 + Tool usage (5 years) (usegalaxy.org.au): 215 + Tool usage (5 years) - all main servers: 1620 + Tool usage (all time) (usegalaxy.eu): 1159 + Tool usage (all time) (usegalaxy.org): 255 + Tool usage (all time) (usegalaxy.org.au): 215 + Tool usage (all time) - all main servers: 1629 + ToolShed categories: + - Computational chemistry + ToolShed id: bio3d + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 5 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 4 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 4 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 4 + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.no: 5 + UseGalaxy.or: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 0 + Conda id: scipy + Conda version: null + Date of first commit of the suite: '2020-01-30' + Description: Tools for MD analysis + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - biomd_neqgamma + - fastpca + - biomd_extract_clusters + - biomd_rmsd_clustering + Galaxy wrapper id: biomoldyn + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ + Galaxy wrapper version: 1.5.2 + No. of tool users (5 years) (usegalaxy.eu): 493 + No. of tool users (5 years) (usegalaxy.org): 441 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 934 + No. of tool users (all time) (usegalaxy.eu): 493 + No. of tool users (all time) (usegalaxy.org): 441 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 934 + Source: https://github.com/moldyn/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 119 + Tool usage (5 years) (usegalaxy.org): 148 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 267 + Tool usage (all time) (usegalaxy.eu): 119 + Tool usage (all time) (usegalaxy.org): 148 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 267 + ToolShed categories: + - Molecular Dynamics + - Computational chemistry + ToolShed id: biomoldyn + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 3 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.no: 3 + UseGalaxy.or: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 7 + Available on UseGalaxy.org.au: 2 + Conda id: ambertools + Conda version: null + Date of first commit of the suite: '2020-04-03' + Description: Ambertools is a set of packages for preparing systems for molecular + dynamics (MD) simulations and analyzing trajectories. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ambertools_acpype + - acpype_Amber2Gromacs + - ambertools_antechamber + - mmpbsa_mmgbsa + - ambertools_parmchk2 + - parmconv + - tleap + Galaxy wrapper id: ambertools + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ + Galaxy wrapper version: '21.10' + No. of tool users (5 years) (usegalaxy.eu): 41793 + No. of tool users (5 years) (usegalaxy.org): 1126 + No. of tool users (5 years) (usegalaxy.org.au): 1552 + No. of tool users (5 years) - all main servers: 44471 + No. of tool users (all time) (usegalaxy.eu): 41881 + No. of tool users (all time) (usegalaxy.org): 1126 + No. of tool users (all time) (usegalaxy.org.au): 1552 + No. of tool users (all time) - all main servers: 44559 + Source: http://ambermd.org/AmberTools.php + Status: To update + Tool usage (5 years) (usegalaxy.eu): 510 + Tool usage (5 years) (usegalaxy.org): 159 + Tool usage (5 years) (usegalaxy.org.au): 85 + Tool usage (5 years) - all main servers: 754 + Tool usage (all time) (usegalaxy.eu): 511 + Tool usage (all time) (usegalaxy.org): 159 + Tool usage (all time) (usegalaxy.org.au): 85 + Tool usage (all time) - all main servers: 755 + ToolShed categories: + - Molecular Dynamics + - Computational chemistry + ToolShed id: ambertools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 2 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 7 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + UseGalaxy.fr: 2 + UseGalaxy.no: 5 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: packmol + Conda version: null + Date of first commit of the suite: '2018-10-04' + Description: PACKMOL is a package for creating starting structures for Molecular + Dynamics simulations + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - packmol + Galaxy wrapper id: packmol + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem + Galaxy wrapper version: 18.169.1 + No. of tool users (5 years) (usegalaxy.eu): 282 + No. of tool users (5 years) (usegalaxy.org): 420 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 702 + No. of tool users (all time) (usegalaxy.eu): 295 + No. of tool users (all time) (usegalaxy.org): 420 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 715 + Source: http://m3g.iqm.unicamp.br/packmol/home.shtml + Status: To update + Tool usage (5 years) (usegalaxy.eu): 32 + Tool usage (5 years) (usegalaxy.org): 8 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 40 + Tool usage (all time) (usegalaxy.eu): 33 + Tool usage (all time) (usegalaxy.org): 8 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 41 + ToolShed categories: + - Molecular Dynamics + - Computational chemistry + ToolShed id: packmol + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2021-12-23' + Description: Set of python scripts and associated tool files that can be used to + modify topology files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gromacs_modify_topology + - gromacs_extract_topology + Galaxy wrapper id: topologyeditors + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors + Galaxy wrapper version: '0' + No. of tool users (5 years) (usegalaxy.eu): 57 + No. of tool users (5 years) (usegalaxy.org): 20 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 77 + No. of tool users (all time) (usegalaxy.eu): 57 + No. of tool users (all time) (usegalaxy.org): 20 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 77 + Source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 8 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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gmx_check + - gmx_editconf + - gmx_energy + - gmx_get_builtin_file + - gmx_rg + - gmx_makendx + - gmx_merge_topology_files + - gmx_em + - gmx_restraints + - gmx_rmsd + - gmx_rmsf + - gmx_setup + - gmx_sim + - gmx_solvate + - gmx_trj + Galaxy wrapper id: gromacs + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs + Galaxy wrapper version: '2022' + No. of tool users (5 years) (usegalaxy.eu): 184067 + No. of tool users (5 years) (usegalaxy.org): 9382 + No. of tool users (5 years) (usegalaxy.org.au): 10325 + No. of tool users (5 years) - all main servers: 203774 + No. of tool users (all time) (usegalaxy.eu): 184203 + No. of tool users (all time) (usegalaxy.org): 9382 + No. of tool users (all time) (usegalaxy.org.au): 10325 + No. of tool users (all time) - all main servers: 203910 + Source: https://github.com/gromacs + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3441 + Tool usage (5 years) (usegalaxy.org): 1438 + Tool usage (5 years) (usegalaxy.org.au): 648 + Tool usage (5 years) - 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mdanalysis_angle + - mdanalysis_dihedral + - mdanalysis_distance + - mdanalysis_endtoend + - mdanalysis_extract_rmsd + - mdanalysis_hbonds + - mdanalysis_cosine_analysis + - mdanalysis_ramachandran_protein + - mdanalysis_ramachandran_plot + - mdanalysis_rdf + Galaxy wrapper id: mdanalysis + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 3209 + No. of tool users (5 years) (usegalaxy.org): 182 + No. of tool users (5 years) (usegalaxy.org.au): 397 + No. of tool users (5 years) - all main servers: 3788 + No. of tool users (all time) (usegalaxy.eu): 3268 + No. of tool users (all time) (usegalaxy.org): 182 + No. of tool users (all time) (usegalaxy.org.au): 397 + No. of tool users (all time) - all main servers: 3847 + Source: https://github.com/MDAnalysis/mdanalysis + Status: To update + Tool usage (5 years) (usegalaxy.eu): 318 + Tool usage (5 years) (usegalaxy.org): 51 + Tool usage (5 years) (usegalaxy.org.au): 39 + Tool usage (5 years) - 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md_converter + Galaxy wrapper id: mdfileconverter + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter + Galaxy wrapper version: 1.9.7 + No. of tool users (5 years) (usegalaxy.eu): 26720 + No. of tool users (5 years) (usegalaxy.org): 784 + No. of tool users (5 years) (usegalaxy.org.au): 977 + No. of tool users (5 years) - all main servers: 28481 + No. of tool users (all time) (usegalaxy.eu): 26762 + No. of tool users (all time) (usegalaxy.org): 784 + No. of tool users (all time) (usegalaxy.org.au): 977 + No. of tool users (all time) - all main servers: 28523 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 251 + Tool usage (5 years) (usegalaxy.org): 54 + Tool usage (5 years) (usegalaxy.org.au): 53 + Tool usage (5 years) - all main servers: 358 + Tool usage (all time) (usegalaxy.eu): 253 + Tool usage (all time) (usegalaxy.org): 54 + Tool usage (all time) (usegalaxy.org.au): 53 + Tool usage (all time) - all main servers: 360 + ToolShed categories: + - Molecular Dynamics + - Computational chemistry + ToolShed id: md_converter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: mdtraj + Conda version: null + Date of first commit of the suite: '2019-10-07' + Description: A tool for slicing trajectory files using MDTraj. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - md_slicer + Galaxy wrapper id: mdslicer + Galaxy wrapper owner: chemteam + Galaxy wrapper parsed folder: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer + Galaxy wrapper source: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer + Galaxy wrapper version: 1.9.9 + No. of tool users (5 years) (usegalaxy.eu): 174 + No. of tool users (5 years) (usegalaxy.org): 6 + No. of tool users (5 years) (usegalaxy.org.au): 441 + No. of tool users (5 years) - all main servers: 621 + No. of tool users (all time) (usegalaxy.eu): 174 + No. of tool users (all time) (usegalaxy.org): 6 + No. of tool users (all time) (usegalaxy.org.au): 441 + No. of tool users (all time) - all main servers: 621 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 19 + Tool usage (5 years) (usegalaxy.org): 4 + Tool usage (5 years) (usegalaxy.org.au): 7 + Tool usage (5 years) - all main servers: 30 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 4 + Tool usage (all time) (usegalaxy.org.au): 7 + Tool usage (all time) - 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all main servers: 128 + Tool usage (all time) (usegalaxy.eu): 128 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 128 + ToolShed categories: + - Ecology + ToolShed id: emlassemblyline + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 11 + Tools available on UseGalaxy.fr: 9 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 11 + UseGalaxy.fr: 9 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2023-10-17' + Description: Tools to compute ecoregionalization with BRT model predictions and + clustering. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ecoregion_brt_analysis + - ecoregion_GeoNearestNeighbor + - ecoregion_cluster_estimate + - ecoregion_clara_cluster + - ecoregion_eco_map + - ecoregion_taxa_seeker + Galaxy wrapper id: Ecoregionalization_workflow + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow + Galaxy wrapper version: 0.1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 352 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 352 + No. of tool users (all time) (usegalaxy.eu): 352 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 352 + Source: https://github.com/PaulineSGN/Workflow_Galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 36 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 36 + Tool usage (all time) (usegalaxy.eu): 36 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 36 + ToolShed categories: + - Ecology + ToolShed id: ecoregionalization + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 6 + UseGalaxy.fr: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2023-11-10' + Description: Tools to compute The evolution of the total volume of very large trees, + standing dead wood and dead wood on the ground on an area and the rate of devolution + of the volume of wood favorable to biodiversity by large ecological regions (France). + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - Map_shp + - Mean_geom + - bar_plot + Galaxy wrapper id: Geom_mean_workflow + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow + Galaxy wrapper version: 0.1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 53 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 53 + No. of tool users (all time) (usegalaxy.eu): 53 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 53 + Source: https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom + Status: To update + Tool usage (5 years) (usegalaxy.eu): 18 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 18 + Tool usage (all time) (usegalaxy.eu): 18 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 18 + ToolShed categories: + - Ecology + ToolShed id: Geometric means (Dead wood) + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 5 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-11-13' + Description: Tools to compute and analyse biodiversity metrics + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pampa_communitymetrics + - pampa_presabs + - pampa_glmcomm + - pampa_glmsp + - pampa_plotglm + Galaxy wrapper id: PAMPA + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA + Galaxy wrapper source: https://github.com/ColineRoyaux/PAMPA-Galaxy + Galaxy wrapper version: 0.0.2 + No. of tool users (5 years) (usegalaxy.eu): 1038 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 849 + No. of tool users (5 years) - all main servers: 1887 + No. of tool users (all time) (usegalaxy.eu): 1038 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 849 + No. of tool users (all time) - all main servers: 1887 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 146 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 38 + Tool usage (5 years) - all main servers: 184 + Tool usage (all time) (usegalaxy.eu): 146 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 38 + Tool usage (all time) - all main servers: 184 + ToolShed categories: + - Ecology + ToolShed id: pampa + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 4 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 5 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.no: 4 + UseGalaxy.or: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: bioconductor-sangerseqr + Conda version: 1.38.0 + Date of first commit of the suite: '2021-10-08' + Description: Tool to convert ab1 files into FASTQ files + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ab1_fastq_converter + Galaxy wrapper id: ab1_fastq + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq + Galaxy wrapper source: https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq + Galaxy wrapper version: 1.20.0 + No. of tool users (5 years) (usegalaxy.eu): 49465 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 49465 + No. of tool users (all time) (usegalaxy.eu): 49465 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 49465 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 281 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 281 + Tool usage (all time) (usegalaxy.eu): 281 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 281 + ToolShed categories: + - Convert Formats + ToolShed id: ab1fastq + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-05-14' + Description: A data source tool for downloading datasets via the AquaINFRA Interaction + Platform. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - aquainfra_importer + Galaxy wrapper id: aquainfra_importer + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer + Galaxy wrapper source: https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 75 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 75 + No. of tool users (all time) (usegalaxy.eu): 75 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 75 + Source: https://github.com/AquaINFRA/galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-10-10' + Description: Wrapper for OGC API Processes developed in the AquaINFRA project. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - aquainfra_ogc_api_processes + Galaxy wrapper id: aquainfra_ogc_api_processes + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes + Galaxy wrapper source: https://github.com/AquaINFRA/tools-ecology/tree/master + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/AquaINFRA/galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 3 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2023-03-06' + Description: Compute indicators for turnover boulders fields + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cb_dissim + - cb_ivr + - cb_div + Galaxy wrapper id: champ_blocs + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs + Galaxy wrapper source: https://github.com/Marie59/champ_blocs + Galaxy wrapper version: 0.0.0 + No. of tool users (5 years) (usegalaxy.eu): 183 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 183 + No. of tool users (all time) (usegalaxy.eu): 183 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 183 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 20 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 20 + Tool usage (all time) (usegalaxy.eu): 20 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 20 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 3 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + UseGalaxy.fr: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-bioseq + Conda version: null + Date of first commit of the suite: '2023-04-11' + Description: Tool to compute a consensus sequence from several aligned fasta sequences + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - aligned_to_consensus + Galaxy wrapper id: consensus_from_alignments + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments + Galaxy wrapper source: https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 1184 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1184 + No. of tool users (all time) (usegalaxy.eu): 1184 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1184 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 154 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 154 + Tool usage (all time) (usegalaxy.eu): 154 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 154 + ToolShed categories: + - Sequence Analysis + ToolShed id: consalign + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 1 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 6 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-tangles + Conda version: null + Date of first commit of the suite: '2021-07-27' + Description: Explore data through multiple statistical tools + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tool_anonymization + - ecology_homogeneity_normality + - ecology_beta_diversity + - ecology_link_between_var + - ecology_presence_abs_abund + - ecology_stat_presence_abs + Galaxy wrapper id: data_exploration + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration + Galaxy wrapper source: https://github.com/Marie59/Data_explo_tools + Galaxy wrapper version: 0.0.0 + No. of tool users (5 years) (usegalaxy.eu): 967 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 967 + No. of tool users (all time) (usegalaxy.eu): 967 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 967 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 308 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 308 + Tool usage (all time) (usegalaxy.eu): 308 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 308 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 6 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.fr: 6 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 5 + Available on UseGalaxy.org.au: 2 + Conda id: xarray + Conda version: null + Date of first commit of the suite: '2022-07-06' + Description: "xarray (formerly xray) is an open source project and Python package\ + \ that makes working withlabelled multi-dimensional arrays simple, efficient,\ + \ and fun!xarray integrates with Dask to support parallel computations and streaming\ + \ computation on datasetsthat don\u2019t fit into memory." + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - timeseries_extraction + - xarray_coords_info + - xarray_mapplot + - xarray_metadata_info + - xarray_netcdf2netcdf + - xarray_select + Galaxy wrapper id: xarray + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ + Galaxy wrapper version: 2022.3.0 + No. of tool users (5 years) (usegalaxy.eu): 5995 + No. of tool users (5 years) (usegalaxy.org): 66 + No. of tool users (5 years) (usegalaxy.org.au): 295 + No. of tool users (5 years) - all main servers: 6356 + No. of tool users (all time) (usegalaxy.eu): 5995 + No. of tool users (all time) (usegalaxy.org): 66 + No. of tool users (all time) (usegalaxy.org.au): 295 + No. of tool users (all time) - all main servers: 6356 + Source: http://xarray.pydata.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 275 + Tool usage (5 years) (usegalaxy.org): 23 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 301 + Tool usage (all time) (usegalaxy.eu): 275 + Tool usage (all time) (usegalaxy.org): 23 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 301 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 6 + Tools available on UseGalaxy.eu: 6 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 2 + Tools available on UseGalaxy.org (Main): 5 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 6 + UseGalaxy.eu: 6 + UseGalaxy.fr: 5 + UseGalaxy.no: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 8 + Available on UseGalaxy.fr: 8 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2019-02-25' + Description: Geospatial Data Abstraction Library tools are all dedicated to manipulate + raster and vector geospatial data formats. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gdal_gdal_merge + - gdal_gdal_translate + - gdal_gdaladdo + - gdal_gdalbuildvrt + - gdal_gdalinfo + - gdal_gdalwarp + - gdal_ogr2ogr + - gdal_ogrinfo + Galaxy wrapper id: gdal + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal + Galaxy wrapper version: 3.0.0 + No. of tool users (5 years) (usegalaxy.eu): 1409 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1409 + No. of tool users (all time) (usegalaxy.eu): 1498 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1498 + Source: https://www.gdal.org + Status: To update + Tool usage (5 years) (usegalaxy.eu): 39 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 39 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 42 + ToolShed categories: + - Ecology + ToolShed id: gdal + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 8 + Tools available on UseGalaxy.eu: 8 + Tools available on UseGalaxy.fr: 8 + Tools available on UseGalaxy.no: 8 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 8 + UseGalaxy.eu: 8 + UseGalaxy.fr: 8 + UseGalaxy.no: 8 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-06-07' + Description: This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hirondelle_crim + Galaxy wrapper id: hirondelle_crim_ogc_api_processes + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 18 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 18 + No. of tool users (all time) (usegalaxy.eu): 18 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 18 + Source: https://github.com/AquaINFRA/galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-getopt + Conda version: null + Date of first commit of the suite: '2024-01-05' + Description: Run IDW interpolation based on a .csv and .geojson file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - interpolation_run_idw_interpolation + Galaxy wrapper id: interpolation + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 70 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 70 + No. of tool users (all time) (usegalaxy.eu): 70 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 70 + Source: https://github.com/AquaINFRA/galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 7 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 7 + Tool usage (all time) (usegalaxy.eu): 7 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 7 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-10-15' + Description: This tool derived from the R Shiny App MetaShRIMPS + is made to produce draft of data paper from Ecological Metadata Language (EML) + based metadata documents. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - data_paper_from_EML + Galaxy wrapper id: make_data_paper_sketches + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches + Galaxy wrapper version: 0.1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/TanguyGen/emldown + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Ecology + ToolShed id: Make data paper sketches from EML + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: sanntis + Conda version: 0.9.3.5 + Date of first commit of the suite: '2024-07-26' + Description: The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic + & metagenomic data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sanntis_marine + Galaxy wrapper id: marine_omics + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics + Galaxy wrapper version: 0.9.3.5 + No. of tool users (5 years) (usegalaxy.eu): 51 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 51 + No. of tool users (all time) (usegalaxy.eu): 51 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 51 + Source: https://github.com/Finn-Lab/SanntiS + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pandas + Conda version: null + Date of first commit of the suite: '2023-12-12' + Description: Retrieve environmental data from etopo, cmems and woa + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - iabiodiv_smartbiodiv_med_environ + Galaxy wrapper id: medenv + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv + Galaxy wrapper source: https://github.com/jeremyfix/medenv + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 27 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 27 + No. of tool users (all time) (usegalaxy.eu): 27 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 27 + Source: https://github.com/jeremyfix/medenv + Status: To update + Tool usage (5 years) (usegalaxy.eu): 9 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 9 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Ecology + - Data Source + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2022-11-04' + Description: Compute biodiveristy indicators for marine data from obis + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - obisindicators + - obis_data + Galaxy wrapper id: obisindicators + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators + Galaxy wrapper version: 0.0.2 + No. of tool users (5 years) (usegalaxy.eu): 352 + No. of tool users (5 years) (usegalaxy.org): 8 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 360 + No. of tool users (all time) (usegalaxy.eu): 352 + No. of tool users (all time) (usegalaxy.org): 8 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 360 + Source: https://github.com/Marie59/obisindicators + Status: To update + Tool usage (5 years) (usegalaxy.eu): 42 + Tool usage (5 years) (usegalaxy.org): 6 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 48 + Tool usage (all time) (usegalaxy.eu): 42 + Tool usage (all time) (usegalaxy.org): 6 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 48 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: julia + Conda version: null + Date of first commit of the suite: '2023-11-17' + Description: Access, process, visualise oceanographic data for the Earth System + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - argo_getdata + - divand_full_analysis + Galaxy wrapper id: ocean + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean + Galaxy wrapper version: 0.1.15 + No. of tool users (5 years) (usegalaxy.eu): 54 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 54 + No. of tool users (all time) (usegalaxy.eu): 54 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 54 + Source: https://github.com/Marie59/FE-ft-ESG/tree/main/argo + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-03-12' + Description: Outputs a monoband image which is the result of a mathematical operation + on several multi-band images. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - otb_band_math + Galaxy wrapper id: ogcProcess_otb_bandmath + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 98 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 98 + No. of tool users (all time) (usegalaxy.eu): 98 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 98 + Source: https://github.com/AquaINFRA/galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-03-12' + Description: This application smooths an image using the MeanShift algorithm. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - otb_mean_shift_smoothing + Galaxy wrapper id: ogcProcess_otb_meanShiftSmoothing + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation + Galaxy wrapper version: '1.0' + No. of tool users (5 years) (usegalaxy.eu): 57 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 57 + No. of tool users (all time) (usegalaxy.eu): 57 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 57 + Source: https://github.com/AquaINFRA/galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 7 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-mgcv + Conda version: null + Date of first commit of the suite: '2019-06-18' + Description: null + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - regionalgam_ab_index + - regionalgam_autocor_acf + - regionalgam_flight_curve + - regionalgam_glmmpql + - regionalgam_gls_adjusted + - regionalgam_gls + - regionalgam_plot_trend + Galaxy wrapper id: regionalgam + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam + Galaxy wrapper version: '1.5' + No. of tool users (5 years) (usegalaxy.eu): 438 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 438 + No. of tool users (all time) (usegalaxy.eu): 542 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 542 + Source: https://github.com/RetoSchmucki/regionalGAM + Status: To update + Tool usage (5 years) (usegalaxy.eu): 128 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 128 + Tool usage (all time) (usegalaxy.eu): 157 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 157 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 6 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 7 + Tools available on UseGalaxy.no: 7 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 6 + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + UseGalaxy.fr: 7 + UseGalaxy.no: 7 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-06-21' + Description: Search a list of sequences in BOLD (Barcode of Life Data System) from + specified taxa list and markers + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - retrieve_bold + Galaxy wrapper id: retrieve_bold + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold + Galaxy wrapper source: https://github.com/wpearman1996/MARES_database_pipeline/tree/master + Galaxy wrapper version: 1.3.0 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1 + Source: https://anaconda.org/conda-forge/r-bold + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Ecology + ToolShed id: retrieve_bold + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-03-29' + Description: Terrestrial and marine predictors for species distribution modelling. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sdmpredictors_list_layers + Galaxy wrapper id: sdmpredictors + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors + Galaxy wrapper version: 0.2.15 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1 + Source: https://cran.r-project.org/web/packages/sdmpredictors/index.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Ecology + ToolShed id: sdmpredictors + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2019-05-23' + Description: Get species occurences data + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - spocc_occ + Galaxy wrapper id: spocc + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc + Galaxy wrapper version: 1.2.2 + No. of tool users (5 years) (usegalaxy.eu): 789 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 789 + No. of tool users (all time) (usegalaxy.eu): 840 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 840 + Source: https://cran.r-project.org/web/packages/spocc/index.html + Status: To update + Tool usage (5 years) (usegalaxy.eu): 130 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 130 + Tool usage (all time) (usegalaxy.eu): 134 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 134 + ToolShed categories: + - Ecology + ToolShed id: spocc_occ + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 1 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 7 + Available on UseGalaxy.org (Main): 4 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2022-12-30' + Description: Compute biodiversity indicators for remote sensing data from Sentinel + 2 + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - srs_diversity_maps + - srs_global_indices + - srs_process_data + - srs_spectral_indices + - srs_pca + - srs_preprocess_s2 + - srs_metadata + Galaxy wrapper id: srs_tools + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools + Galaxy wrapper source: https://github.com/Marie59/Sentinel_2A/srs_tools + Galaxy wrapper version: 0.0.1 + No. of tool users (5 years) (usegalaxy.eu): 239 + No. of tool users (5 years) (usegalaxy.org): 44 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 283 + No. of tool users (all time) (usegalaxy.eu): 239 + No. of tool users (all time) (usegalaxy.org): 44 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 283 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 34 + Tool usage (5 years) (usegalaxy.org): 13 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 47 + Tool usage (all time) (usegalaxy.eu): 34 + Tool usage (all time) (usegalaxy.org): 13 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 47 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 7 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 7 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 7 + UseGalaxy.eu: 7 + UseGalaxy.fr: 7 + UseGalaxy.or: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 5 + Available on UseGalaxy.fr: 5 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-03-27' + Description: Tools to analyse STOC data. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - stoceps_filteringsp + - stoceps_glm + - stoceps_glm_group + - stoceps_maketablecarrer + - stoceps_trend_indic + Galaxy wrapper id: stoc + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc + Galaxy wrapper source: https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc + Galaxy wrapper version: 0.0.2 + No. of tool users (5 years) (usegalaxy.eu): 328 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 328 + No. of tool users (all time) (usegalaxy.eu): 328 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 328 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 38 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 38 + Tool usage (all time) (usegalaxy.eu): 38 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 38 + ToolShed categories: + - Ecology + ToolShed id: stoceps + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 5 + Tools available on UseGalaxy.eu: 5 + Tools available on UseGalaxy.fr: 5 + Tools available on UseGalaxy.no: 5 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 5 + UseGalaxy.eu: 5 + UseGalaxy.fr: 5 + UseGalaxy.no: 5 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 4 + Available on UseGalaxy.fr: 4 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2019-03-13' + Description: Tools created by the vigiechiro team to analyses and identify chiro + sounds files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - vigiechiro_bilanenrichipf + - vigiechiro_bilanenrichirp + - vigiechiro_idcorrect_2ndlayer + - vigiechiro_idvalid + Galaxy wrapper id: vigiechiro + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro + Galaxy wrapper version: 0.1.1 + No. of tool users (5 years) (usegalaxy.eu): 14412 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 14412 + No. of tool users (all time) (usegalaxy.eu): 14590 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 14590 + Source: https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro + Status: To update + Tool usage (5 years) (usegalaxy.eu): 722 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 722 + Tool usage (all time) (usegalaxy.eu): 732 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 732 + ToolShed categories: + - Ecology + ToolShed id: vigiechiro + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 4 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 4 + Tools available on UseGalaxy.no: 4 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 4 + UseGalaxy.eu: 4 + UseGalaxy.fr: 4 + UseGalaxy.no: 4 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: xmlstarlet + Conda version: null + Date of first commit of the suite: '2021-10-18' + Description: Tool to convert a xml file from one metadata standard to another + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - xmlstarlet + Galaxy wrapper id: xmlstarlet + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet + Galaxy wrapper version: 1.6.1 + No. of tool users (5 years) (usegalaxy.eu): 59 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 59 + No. of tool users (all time) (usegalaxy.eu): 59 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 59 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 17 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 17 + ToolShed categories: + - Convert Formats + ToolShed id: xmlstarlet + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-base + Conda version: null + Date of first commit of the suite: '2024-05-03' + Description: This tool is a wrapper for OGC API Processes (OTB) coming from the + Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using + the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). + Check the README in the repository for more information. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - zoo_project_ogc_api_processes + Galaxy wrapper id: zoo_project_ogc_api_processes + Galaxy wrapper owner: ecology + Galaxy wrapper parsed folder: https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes + Galaxy wrapper source: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 26 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 26 + No. of tool users (all time) (usegalaxy.eu): 26 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 26 + Source: https://github.com/AquaINFRA/galaxy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Ecology + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2021-04-13' + Description: Copernicus Climate Change Service (C3S) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - c3s + Galaxy wrapper id: c3s + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s + Galaxy wrapper version: 0.3.0 + No. of tool users (5 years) (usegalaxy.eu): 234 + No. of tool users (5 years) (usegalaxy.org): 4 + No. of tool users (5 years) (usegalaxy.org.au): 92 + No. of tool users (5 years) - all main servers: 330 + No. of tool users (all time) (usegalaxy.eu): 234 + No. of tool users (all time) (usegalaxy.org): 4 + No. of tool users (all time) (usegalaxy.org.au): 92 + No. of tool users (all time) - all main servers: 330 + Source: https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 4 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 18 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 4 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 18 + ToolShed categories: + - Climate Analysis + ToolShed id: c3s + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2021-06-19' + Description: Copernicus Atmosphere Data Store (ADS) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cads + Galaxy wrapper id: cads + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 52 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 52 + No. of tool users (all time) (usegalaxy.eu): 52 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 52 + Source: https://ads.atmosphere.copernicus.eu/#!/home + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Climate Analysis + ToolShed id: cads + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2021-09-01' + Description: CDO (Climate Data Operators) is a collection of command line Operators + to manipulate and analyse Climate and NWP model Data.Supported data formats are + GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators + available. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cdo_info + - cdo_operations + Galaxy wrapper id: cdo + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo + Galaxy wrapper version: 2.0.0 + No. of tool users (5 years) (usegalaxy.eu): 218 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 218 + No. of tool users (all time) (usegalaxy.eu): 218 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 218 + Source: https://code.mpimet.mpg.de/projects/cdo/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 17 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 17 + Tool usage (all time) (usegalaxy.eu): 17 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 17 + ToolShed categories: + - Climate Analysis + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: cesm + Conda version: 2.1.3 + Date of first commit of the suite: '2021-06-15' + Description: Community Earth System Model (CESM) + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cesm + Galaxy wrapper id: cesm + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm + Galaxy wrapper source: https://github.com/ESCOMP/CESM + Galaxy wrapper version: 2.1.3 + No. of tool users (5 years) (usegalaxy.eu): 14 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 14 + No. of tool users (all time) (usegalaxy.eu): 14 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 14 + Source: https://www.cesm.ucar.edu/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Climate Analysis + ToolShed id: cesm + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-10-05' + Description: Create climate stripes from a tabular input file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - climate_stripes + Galaxy wrapper id: climate-stripes + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 239 + No. of tool users (5 years) (usegalaxy.org): 16 + No. of tool users (5 years) (usegalaxy.org.au): 182 + No. of tool users (5 years) - all main servers: 437 + No. of tool users (all time) (usegalaxy.eu): 239 + No. of tool users (all time) (usegalaxy.org): 16 + No. of tool users (all time) (usegalaxy.org.au): 182 + No. of tool users (all time) - all main servers: 437 + Source: https://www.climate-lab-book.ac.uk/2018/warming-stripes/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 35 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 3 + Tool usage (5 years) - all main servers: 40 + Tool usage (all time) (usegalaxy.eu): 35 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 3 + Tool usage (all time) - all main servers: 40 + ToolShed categories: + - Climate Analysis + - Visualization + ToolShed id: climate_stripes + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: eodie + Conda version: null + Date of first commit of the suite: '2021-12-30' + Description: Earth Observation Data Information Extractor + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - eodie + Galaxy wrapper id: eodie + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie + Galaxy wrapper source: https://gitlab.com/eetun-tiimi/EODIE + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 45 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 45 + No. of tool users (all time) (usegalaxy.eu): 45 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 45 + Source: https://eodie.readthedocs.io/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Climate Analysis + ToolShed id: eodie + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-05-03' + Description: Get Copernicus Essential Climate Variables for assessing climate variability + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cds_essential_variability + Galaxy wrapper id: essential_climate_variables + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 232 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 232 + No. of tool users (all time) (usegalaxy.eu): 336 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 336 + Source: https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview + Status: To update + Tool usage (5 years) (usegalaxy.eu): 39 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 39 + Tool usage (all time) (usegalaxy.eu): 40 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 40 + ToolShed categories: + - Climate Analysis + - Data Source + ToolShed id: cds_essential_variability + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: fates-emerald + Conda version: null + Date of first commit of the suite: '2020-10-21' + Description: EMERALD version of the Functionally Assembled Terrestrial Ecosystem + Simulator (FATES) with Community Terrestrial Systems Model as host model + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ctsm_fates + Galaxy wrapper id: fates-emerald + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald + Galaxy wrapper version: '2.0' + No. of tool users (5 years) (usegalaxy.eu): 264 + No. of tool users (5 years) (usegalaxy.org): 34 + No. of tool users (5 years) (usegalaxy.org.au): 103 + No. of tool users (5 years) - all main servers: 401 + No. of tool users (all time) (usegalaxy.eu): 264 + No. of tool users (all time) (usegalaxy.org): 34 + No. of tool users (all time) (usegalaxy.org.au): 103 + No. of tool users (all time) - all main servers: 401 + Source: https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api + Status: To update + Tool usage (5 years) (usegalaxy.eu): 69 + Tool usage (5 years) (usegalaxy.org): 11 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 81 + Tool usage (all time) (usegalaxy.eu): 69 + Tool usage (all time) (usegalaxy.org): 11 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 81 + ToolShed categories: + - Climate Analysis + ToolShed id: ctsm_fates + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-03-15' + Description: Creates a png image showing statistic over areas as defined in the + vector file + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mean_per_zone + Galaxy wrapper id: mean-per-zone + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 20 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 20 + No. of tool users (all time) (usegalaxy.eu): 25 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 25 + Source: https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 3 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 3 + Tool usage (all time) (usegalaxy.eu): 3 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 3 + ToolShed categories: + - Visualization + - GIS + - Climate Analysis + ToolShed id: mean_per_zone + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-10-04' + Description: Visualization of regular geographical data on a map with psyplot + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - psy_maps + Galaxy wrapper id: psy-maps + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps + Galaxy wrapper version: 1.3.1 + No. of tool users (5 years) (usegalaxy.eu): 333 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 333 + No. of tool users (all time) (usegalaxy.eu): 502 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 502 + Source: https://github.com/Chilipp/psy-maps + Status: To update + Tool usage (5 years) (usegalaxy.eu): 62 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 62 + Tool usage (all time) (usegalaxy.eu): 62 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 62 + ToolShed categories: + - Visualization + - Climate Analysis + ToolShed id: psy_maps + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: python + Conda version: null + Date of first commit of the suite: '2019-03-15' + Description: Shift longitudes ranging from 0. and 360 degrees to -180. and 180. + degrees + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - shyft_longitudes + Galaxy wrapper id: shift-longitudes + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 54 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 54 + No. of tool users (all time) (usegalaxy.eu): 64 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 64 + Source: https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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smithsonian_volcanoes + Galaxy wrapper id: smithsonian-volcanoes + Galaxy wrapper owner: climate + Galaxy wrapper parsed folder: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes + Galaxy wrapper source: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://volcano.si.edu/gvp_votw.cfm + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Retrieve Data + ToolShed id: smithsonian_volcanoes + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: scxa-plots + Conda version: 0.0.1 + Date of first commit of the suite: '2019-11-07' + Description: Make a cell barcode plot for droplet single-cell RNA-seq QC + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - _dropletBarcodePlot + Galaxy wrapper id: droplet-barcode-plot + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml + Galaxy wrapper version: 1.6.1+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 1151 + No. of tool users (5 years) (usegalaxy.org): 356 + No. of tool users (5 years) (usegalaxy.org.au): 3 + No. of tool users (5 years) - all main servers: 1510 + No. of tool users (all time) (usegalaxy.eu): 1151 + No. of tool users (all time) (usegalaxy.org): 356 + No. of tool users (all time) (usegalaxy.org.au): 3 + No. of tool users (all time) - all main servers: 1510 + Source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary + Status: To update + Tool usage (5 years) (usegalaxy.eu): 184 + Tool usage (5 years) (usegalaxy.org): 77 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - 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fastq_provider + Galaxy wrapper id: fastq_provider + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider + Galaxy wrapper version: 0.4.4 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/ebi-gene-expression-group/atlas-fastq-provider + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Data Source + - RNA + - Transcriptomics + ToolShed id: atlas_fastq_provider + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: atlas-gene-annotation-manipulation + Conda version: 1.1.1 + Date of first commit of the suite: '2019-11-07' + Description: Utility to extract annotations from Ensembl GTF files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - _ensembl_gtf2gene_list + Galaxy wrapper id: gtf-2-gene-list + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml + Galaxy wrapper version: 1.52.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 1982 + No. of tool users (5 years) (usegalaxy.org): 1040 + No. of tool users (5 years) (usegalaxy.org.au): 205 + No. of tool users (5 years) - all main servers: 3227 + No. of tool users (all time) (usegalaxy.eu): 1983 + No. of tool users (all time) (usegalaxy.org): 1040 + No. of tool users (all time) (usegalaxy.org.au): 205 + No. of tool users (all time) - all main servers: 3228 + Source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary + Status: To update + Tool usage (5 years) (usegalaxy.eu): 323 + Tool usage (5 years) (usegalaxy.org): 343 + Tool usage (5 years) (usegalaxy.org.au): 38 + Tool usage (5 years) - 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fastq_pair + Galaxy wrapper id: fastq_pair + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair + Galaxy wrapper version: 1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/linsalrob/fastq-pair + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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cshl_fastq_quality_trimmer + Galaxy wrapper id: fastq_quality_trimmer + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer + Galaxy wrapper version: 0.0.14+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/agordon/fastx_toolkit + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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fastq_filter_n + - fastq_trim_poly_at + Galaxy wrapper id: fastq_utils + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils + Galaxy wrapper version: 0.25.1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/nunofonseca/fastq_utils + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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ct_build_cell_ontology_dict + - ct_check_labels + - ct_combine_tool_outputs + - ct_downsample_cells + - ct_get_consensus_outputs + - ct_get_empirical_dist + - ct_get_tool_perf_table + - ct_get_tool_pvals + Galaxy wrapper id: cell-types-analysis + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 1.1.1 + No. of tool users (5 years) (usegalaxy.eu): 8 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 8 + No. of tool users (all time) (usegalaxy.eu): 8 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 8 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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hca_matrix_downloader + Galaxy wrapper id: data-hca + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: v0.0.4+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 441 + No. of tool users (5 years) (usegalaxy.org): 3 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 444 + No. of tool users (all time) (usegalaxy.eu): 451 + No. of tool users (all time) (usegalaxy.org): 3 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 454 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 83 + Tool usage (5 years) (usegalaxy.org): 2 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 85 + Tool usage (all time) (usegalaxy.eu): 87 + Tool usage (all time) (usegalaxy.org): 2 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 89 + ToolShed categories: + - Transcriptomics + - Sequence Analysis + ToolShed id: suite_human_cell_atlas_tools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: wget + Conda version: null + Date of first commit of the suite: '2019-07-02' + Description: Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home + https://www.ebi.ac.uk/gxa/sc/home + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - retrieve_scxa + Galaxy wrapper id: data-scxa + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: v0.0.2+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 867 + No. of tool users (5 years) (usegalaxy.org): 339 + No. of tool users (5 years) (usegalaxy.org.au): 64 + No. of tool users (5 years) - all main servers: 1270 + No. of tool users (all time) (usegalaxy.eu): 877 + No. of tool users (all time) (usegalaxy.org): 339 + No. of tool users (all time) (usegalaxy.org.au): 64 + No. of tool users (all time) - all main servers: 1280 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 213 + Tool usage (5 years) (usegalaxy.org): 94 + Tool usage (5 years) (usegalaxy.org.au): 5 + Tool usage (5 years) - all main servers: 312 + Tool usage (all time) (usegalaxy.eu): 216 + Tool usage (all time) (usegalaxy.org): 94 + Tool usage (all time) (usegalaxy.org.au): 5 + Tool usage (all time) - all main servers: 315 + ToolShed categories: + - Transcriptomics + - Sequence Analysis + ToolShed id: suite_ebi_expression_atlas + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: decoupler + Conda version: 1.5.0 + Date of first commit of the suite: '2023-09-24' + Description: decoupler - Ensemble of methods to infer biological activities + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - score_genes_aucell + - decoupler_pathway_inference + - decoupler_pseudobulk + Galaxy wrapper id: decoupler + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 1.4.0+galaxy3 + No. of tool users (5 years) (usegalaxy.eu): 54 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 54 + No. of tool users (all time) (usegalaxy.eu): 54 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 54 + Source: https://decoupler-py.readthedocs.io/en/latest/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Transcriptomics + ToolShed id: suite_decoupler + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: dropletutils-scripts + Conda version: 0.0.5 + Date of first commit of the suite: '2019-01-22' + Description: De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts + and DropletUtils 1.0.3 + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - dropletutils_empty_drops + - dropletutils_read_10x + Galaxy wrapper id: dropletutils + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 1.0.4 + No. of tool users (5 years) (usegalaxy.eu): 1900 + No. of tool users (5 years) (usegalaxy.org): 609 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2509 + No. of tool users (all time) (usegalaxy.eu): 1901 + No. of tool users (all time) (usegalaxy.org): 609 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2510 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 412 + Tool usage (5 years) (usegalaxy.org): 131 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 543 + Tool usage (all time) (usegalaxy.eu): 413 + Tool usage (all time) (usegalaxy.org): 131 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 544 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + - Sequence Analysis + ToolShed id: suite_dropletutils + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: garnett-cli + Conda version: 0.0.5 + Date of first commit of the suite: '2020-04-03' + Description: De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli + and r-garnett 0.2.8 + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - garnett_check_markers + - garnett_classify_cells + - garnett_get_feature_genes + - garnett_get_std_output + - garnett_train_classifier + - garnett_transform_markers + - update_marker_file + Galaxy wrapper id: garnett + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 0.2.8 + No. of tool users (5 years) (usegalaxy.eu): 27 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 27 + No. of tool users (all time) (usegalaxy.eu): 27 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 27 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 11 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 11 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + - Sequence Analysis + ToolShed id: suite_garnett + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 7 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 9 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 9 + Available on UseGalaxy.org.au: 0 + Conda id: monocle3-cli + Conda version: 0.0.9 + Date of first commit of the suite: '2019-09-09' + Description: De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts + and monocle3 0.1.2. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - monocle3_create + - monocle3_diffExp + - monocle3_learnGraph + - monocle3_orderCells + - monocle3_partition + - monocle3_plotCells + - monocle3_preprocess + - monocle3_reduceDim + - monocle3_topmarkers + Galaxy wrapper id: monocle3 + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 0.1.4 + No. of tool users (5 years) (usegalaxy.eu): 3610 + No. of tool users (5 years) (usegalaxy.org): 1728 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5338 + No. of tool users (all time) (usegalaxy.eu): 3610 + No. of tool users (all time) (usegalaxy.org): 1728 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5338 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 559 + Tool usage (5 years) (usegalaxy.org): 434 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 993 + Tool usage (all time) (usegalaxy.eu): 559 + Tool usage (all time) (usegalaxy.org): 434 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 993 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + - Sequence Analysis + ToolShed id: suite_monocle3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 9 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 9 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 9 + UseGalaxy.or: 9 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2024-08-20' + Description: PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - pyscenic_aucell + - pyscenic_binarize + - pyscenic_ctx + - pyscenic_grn + Galaxy wrapper id: pyscenic + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 0.12.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Transcriptomics + - RNA + - Sequence Analysis + ToolShed id: suite_pyscenic + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: sc3-scripts + Conda version: 0.0.6 + Date of first commit of the suite: '2018-11-05' + Description: De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts + and SC3 1.8.0. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sc3_calc_biology + - sc3_calc_consens + - sc3_calc_dists + - sc3_calc_transfs + - sc3_estimate_k + - sc3_kmeans + - sc3_prepare + Galaxy wrapper id: sc3 + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 1.8.0 + No. of tool users (5 years) (usegalaxy.eu): 13 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 13 + No. of tool users (all time) (usegalaxy.eu): 13 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 13 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 10 + Tool usage (all time) (usegalaxy.eu): 10 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 10 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + - Sequence Analysis + ToolShed id: suite_sc3 + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 7 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 7 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 27 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 27 + Available on UseGalaxy.org.au: 27 + Conda id: scanpy-scripts + Conda version: 1.9.301 + Date of first commit of the suite: '2020-09-29' + Description: scanpy-scripts, command-line wrapper scripts around Scanpy. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - anndata_ops + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_find_cluster + - scanpy_find_markers + - scanpy_find_variable_genes + - scanpy_integrate_bbknn + - scanpy_integrate_combat + - scanpy_integrate_harmony + - scanpy_integrate_mnn + - scanpy_plot_scrublet + - scanpy_multiplet_scrublet + - scanpy_compute_graph + - scanpy_normalise_data + - scanpy_parameter_iterator + - scanpy_plot_embed + - scanpy_plot_trajectory + - scanpy_read_10x + - scanpy_regress_variable + - scanpy_run_diffmap + - scanpy_run_dpt + - scanpy_run_fdg + - scanpy_run_paga + - scanpy_run_pca + - scanpy_run_tsne + - scanpy_run_umap + - scanpy_scale_data + Galaxy wrapper id: scanpy + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy + Galaxy wrapper version: 1.9.3 + No. of tool users (5 years) (usegalaxy.eu): 45501 + No. of tool users (5 years) (usegalaxy.org): 7304 + No. of tool users (5 years) (usegalaxy.org.au): 3106 + No. of tool users (5 years) - all main servers: 55911 + No. of tool users (all time) (usegalaxy.eu): 45666 + No. of tool users (all time) (usegalaxy.org): 7304 + No. of tool users (all time) (usegalaxy.org.au): 3106 + No. of tool users (all time) - all main servers: 56076 + Source: https://scanpy.readthedocs.io + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4832 + Tool usage (5 years) (usegalaxy.org): 1846 + Tool usage (5 years) (usegalaxy.org.au): 457 + Tool usage (5 years) - all main servers: 7135 + Tool usage (all time) (usegalaxy.eu): 4868 + Tool usage (all time) (usegalaxy.org): 1846 + Tool usage (all time) (usegalaxy.org.au): 457 + Tool usage (all time) - all main servers: 7171 + ToolShed categories: + - Transcriptomics + - Sequence Analysis + - RNA + ToolShed id: scanpy_scripts + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 14 + Tools available on UseGalaxy.eu: 27 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 13 + Tools available on UseGalaxy.org (Main): 27 + Tools available on UseGalaxy.org.au: 27 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 14 + UseGalaxy.eu: 27 + UseGalaxy.no: 13 + UseGalaxy.or: 27 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 6 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 2 + Conda id: scater-scripts + Conda version: 0.0.5 + Date of first commit of the suite: '2018-10-11' + Description: De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts + and Scater 1.8.4. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - scater_calculate_cpm + - scater_calculate_qc_metrics + - scater_filter + - scater_is_outlier + - scater_normalize + - scater_read_10x_results + Galaxy wrapper id: scater + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 1.10.0 + No. of tool users (5 years) (usegalaxy.eu): 381 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 297 + No. of tool users (5 years) - all main servers: 678 + No. of tool users (all time) (usegalaxy.eu): 388 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 297 + No. of tool users (all time) - all main servers: 685 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 99 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 9 + Tool usage (5 years) - 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run_sccaf + - sccaf_asses + - sccaf_asses_merger + - sccaf_regress_out + Galaxy wrapper id: sccaf + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf + Galaxy wrapper version: 0.0.9 + No. of tool users (5 years) (usegalaxy.eu): 110 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 110 + No. of tool users (all time) (usegalaxy.eu): 110 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 110 + Source: https://github.com/sccaf/sccaf + Status: To update + Tool usage (5 years) (usegalaxy.eu): 19 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 19 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 19 + ToolShed categories: + - Transcriptomics + ToolShed id: SCCAF + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 4 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 4 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 4 + UseGalaxy.or: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-sceasy + Conda version: 0.0.7 + Date of first commit of the suite: '2019-10-14' + Description: Convert scRNA data object between popular formats + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sceasy_convert + Galaxy wrapper id: sceasy + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 0.0.5 + No. of tool users (5 years) (usegalaxy.eu): 1059 + No. of tool users (5 years) (usegalaxy.org): 426 + No. of tool users (5 years) (usegalaxy.org.au): 1 + No. of tool users (5 years) - all main servers: 1486 + No. of tool users (all time) (usegalaxy.eu): 1059 + No. of tool users (all time) (usegalaxy.org): 426 + No. of tool users (all time) (usegalaxy.org.au): 1 + No. of tool users (all time) - all main servers: 1486 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 222 + Tool usage (5 years) (usegalaxy.org): 71 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 294 + Tool usage (all time) (usegalaxy.eu): 222 + Tool usage (all time) (usegalaxy.org): 71 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 294 + ToolShed categories: + - Transcriptomics + ToolShed id: sceasy + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 1 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 7 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: scmap-cli + Conda version: 0.1.0 + Date of first commit of the suite: '2019-08-30' + Description: De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli + and scmap 1.6.0. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - scmap_get_std_output + - scmap_index_cell + - scmap_index_cluster + - scmap_preprocess_sce + - scmap_scmap_cell + - scmap_scmap_cluster + - scmap_select_features + Galaxy wrapper id: scmap + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 1.6.4 + No. of tool users (5 years) (usegalaxy.eu): 97 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 97 + No. of tool users (all time) (usegalaxy.eu): 97 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 97 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 41 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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scpred_get_feature_space + - scpred_get_std_output + - scpred_predict_labels + - scpred_train_model + Galaxy wrapper id: scpred + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Galaxy wrapper version: 1.0.2 + No. of tool users (5 years) (usegalaxy.eu): 25 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 25 + No. of tool users (all time) (usegalaxy.eu): 25 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 25 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - 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seurat_convert + - seurat_dim_plot + - seurat_export_cellbrowser + - seurat_filter_cells + - seurat_find_clusters + - seurat_find_markers + - seurat_find_neighbours + - seurat_find_variable_genes + - seurat_hover_locator + - seurat_integration + - seurat_map_query + - seurat_normalise_data + - seurat_plot + - seurat_read10x + - seurat_run_pca + - seurat_run_tsne + - seurat_run_umap + - seurat_scale_data + - seurat_select_integration_features + Galaxy wrapper id: seurat + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat + Galaxy wrapper source: null + Galaxy wrapper version: 4.0.0 + No. of tool users (5 years) (usegalaxy.eu): 2296 + No. of tool users (5 years) (usegalaxy.org): 141 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 2437 + No. of tool users (all time) (usegalaxy.eu): 2328 + No. of tool users (all time) (usegalaxy.org): 141 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 2469 + Source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 673 + Tool usage (5 years) (usegalaxy.org): 39 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 712 + Tool usage (all time) (usegalaxy.eu): 676 + Tool usage (all time) (usegalaxy.org): 39 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 715 + ToolShed categories: + - Transcriptomics + - RNA + - Statistics + - Sequence Analysis + ToolShed id: suite_seurat + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 19 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 14 + Tools available on UseGalaxy.fr: 11 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 14 + Tools available on UseGalaxy.org.au: 14 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 14 + UseGalaxy.fr: 19 + UseGalaxy.or: 14 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ucsc-cell-browser + Conda version: 1.2.8 + Date of first commit of the suite: '2018-09-11' + Description: Python pipeline and Javascript scatter plot library for single-cell + datasets + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - ucsc_cell_browser + Galaxy wrapper id: ucsc-cell-browser + Galaxy wrapper owner: ebi-gxa + Galaxy wrapper parsed folder: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser + Galaxy wrapper source: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml + Galaxy wrapper version: 1.0.0+galaxy1 + No. of tool users (5 years) (usegalaxy.eu): 965 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 965 + No. of tool users (all time) (usegalaxy.eu): 975 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 975 + Source: https://cells.ucsc.edu/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 178 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 178 + Tool usage (all time) (usegalaxy.eu): 181 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 181 + ToolShed categories: + - Transcriptomics + ToolShed id: ucsc_cell_browser + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 1 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.no: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: biotransformer + Conda version: 3.0.20230403 + Date of first commit of the suite: '2020-12-11' + Description: BioTransformer is a tool for prediction of small molecule metabolism + in mammals. + EDAM operation: + - Metabolic pathway prediction + - PTM site prediction + - Natural product identification + EDAM operation (no superclasses): + - Metabolic pathway prediction + - PTM site prediction + - Natural product identification + EDAM topic: + - Small molecules + - Endocrinology and metabolism + - Metabolomics + - Carbohydrates + - NMR + EDAM topic (no superclasses): + - Small molecules + - Endocrinology and metabolism + - Metabolomics + - Carbohydrates + - NMR + Galaxy tool ids: + - biotransformer + Galaxy wrapper id: biotransformer + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer + Galaxy wrapper version: 3.0.20230403 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 48 + No. of tool users (5 years) - all main servers: 48 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 48 + No. of tool users (all time) - all main servers: 48 + Source: https://bitbucket.org/djoumbou/biotransformerjar/src/master/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Metabolomics + ToolShed id: biotransformer + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: BioTransformer is a freely available web server that supports + accurate, rapid and comprehensive in silico metabolism prediction. + bio.tool id: biotransformer + bio.tool ids: + - biotransformer + bio.tool name: BioTransformer +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: openbabel + Conda version: 2.3.90dev7d621d9 + Date of first commit of the suite: '2021-01-06' + Description: Tool for filtering organometallics/anorganic compounds from a list + of compounds. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - filter_orgmet_anorg + Galaxy wrapper id: filter_compounds + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds + Galaxy wrapper version: 3.1.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/RECETOX/galaxytools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: filter_compounds + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: gc-meox-tms + Conda version: 1.0.1 + Date of first commit of the suite: '2024-03-15' + Description: In silico derivatization for GC. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - gc_derivatization + Galaxy wrapper id: gc_derivatization + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization + Galaxy wrapper version: 1.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/RECETOX/gc-meox-tms + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: gc_derivatization + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: bioconductor-metabocoreutils + Conda version: 1.10.0 + Date of first commit of the suite: '2023-10-26' + Description: Create an isotopic pattern library for given compounds and adducts. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - isolib + Galaxy wrapper id: isolib + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/isolib + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/isolib + Galaxy wrapper version: 1.0.1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/RECETOX/galaxytools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: isolib + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 14 + Available on UseGalaxy.fr: 11 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 14 + Conda id: matchms + Conda version: 0.27.0 + Date of first commit of the suite: '2023-12-12' + Description: Searching, filtering and converting mass spectral libraries. + EDAM operation: + - Spectral library search + - Format validation + - Filtering + EDAM operation (no superclasses): + - Spectral library search + - Format validation + - Filtering + EDAM topic: + - Metabolomics + EDAM topic (no superclasses): + - Metabolomics + Galaxy tool ids: + - matchms_add_key + - matchms_convert + - matchms_filtering + - matchms_fingerprint_similarity + - matchms_formatter + - matchms_metadata_export + - matchms_metadata_match + - matchms_metadata_merge + - matchms_networking + - matchms_remove_key + - matchms_remove_spectra + - matchms_spectral_similarity + - matchms_split + - matchms_subsetting + Galaxy wrapper id: matchms + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/matchms + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/matchms + Galaxy wrapper version: 0.27.0 + No. of tool users (5 years) (usegalaxy.eu): 1620 + No. of tool users (5 years) (usegalaxy.org): 27 + No. of tool users (5 years) (usegalaxy.org.au): 1685 + No. of tool users (5 years) - all main servers: 3332 + No. of tool users (all time) (usegalaxy.eu): 1620 + No. of tool users (all time) (usegalaxy.org): 27 + No. of tool users (all time) (usegalaxy.org.au): 1685 + No. of tool users (all time) - all main servers: 3332 + Source: https://github.com/matchms/matchms + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 70 + Tool usage (5 years) (usegalaxy.org): 8 + Tool usage (5 years) (usegalaxy.org.au): 12 + Tool usage (5 years) - all main servers: 90 + Tool usage (all time) (usegalaxy.eu): 70 + Tool usage (all time) (usegalaxy.org): 8 + Tool usage (all time) (usegalaxy.org.au): 12 + Tool usage (all time) - all main servers: 90 + ToolShed categories: + - Metabolomics + ToolShed id: matchms + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 9 + Tools available on UseGalaxy.eu: 14 + Tools available on UseGalaxy.fr: 11 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 14 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 9 + UseGalaxy.eu: 14 + UseGalaxy.fr: 11 + UseGalaxy.or: 14 + biii: null + bio.tool description: Tool to import, process, clean, and compare mass spectrometry + data. + bio.tool id: matchms + bio.tool ids: + - matchms + bio.tool name: Matchms +- Available on UseGalaxy.eu: 9 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-mfassignr + Conda version: 1.1.1 + Date of first commit of the suite: '2024-08-08' + Description: The MFAssignR package was designed for multi-element molecular formula + (MF) assignment of ultrahigh resolution mass spectrometry measurements + EDAM operation: + - Visualisation + EDAM operation (no superclasses): + - Visualisation + EDAM topic: + - Proteomics experiment + - Molecular interactions, pathways and networks + - Workflows + EDAM topic (no superclasses): + - Proteomics experiment + - Molecular interactions, pathways and networks + - Workflows + Galaxy tool ids: + - mfassignr_findRecalSeries + - mfassignr_histnoise + - mfassignr_isofiltr + - mfassignr_kmdnoise + - mfassignr_mfassign + - mfassignr_mfassignCHO + - mfassignr_recal + - mfassignr_recallist + - mfassignr_snplot + Galaxy wrapper id: mfassignr + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr + Galaxy wrapper version: 1.1.1 + No. of tool users (5 years) (usegalaxy.eu): 10 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 10 + No. of tool users (all time) (usegalaxy.eu): 10 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 10 + Source: https://github.com/RECETOX/MFAssignR + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 8 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 8 + Tool usage (all time) (usegalaxy.eu): 8 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 8 + ToolShed categories: + - Metabolomics + ToolShed id: MFAssignR + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 9 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 9 + biii: null + bio.tool description: Molecular formula assignment software for ultrahigh resolution + mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution + mass spectrometry is widely used for nontargeted analysis of complex environmental + and biological mixtures, such as dissolved organic matter, due to its unparalleled + ability to provide accurate mass measurements. + bio.tool id: mfassignr + bio.tool ids: + - mfassignr + bio.tool name: MFAssignR +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: pandas + Conda version: null + Date of first commit of the suite: '2024-02-16' + Description: null + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - target_screen + - use_theoretical_mz_annotations + Galaxy wrapper id: misc + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/misc + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/misc + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 6 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 6 + No. of tool users (all time) (usegalaxy.eu): 6 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 6 + Source: https://github.com/RECETOX/galaxytools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ms2deepscore + Conda version: 2.2.0 + Date of first commit of the suite: '2024-08-15' + Description: Mass spectra similarity scoring using a trained ms2deepscore model. + EDAM operation: + - Spectrum calculation + - Spectral library search + - Network analysis + EDAM operation (no superclasses): + - Spectrum calculation + - Spectral library search + - Network analysis + EDAM topic: + - Proteomics experiment + - Machine learning + - Metabolomics + - Small molecules + - Compound libraries and screening + EDAM topic (no superclasses): + - Proteomics experiment + - Machine learning + - Metabolomics + - Small molecules + - Compound libraries and screening + Galaxy tool ids: + - ms2deepscore_config_generator + - ms2deepscore_similarity + - ms2deepscore_training + Galaxy wrapper id: ms2deepscore + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore + Galaxy wrapper version: 2.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/matchms/ms2deepscore + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: ms2deepscore + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 3 + biii: null + bio.tool description: MS2DeepScore is a deep learning similarity measure for mass + fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network + that is trained to predict molecular structural similarities (Tanimoto scores) + from pairs of mass spectrometry spectra. + bio.tool id: ms2deepscore + bio.tool ids: + - ms2deepscore + bio.tool name: MS2DeepScore +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: msmetaenhancer + Conda version: 0.4.0 + Date of first commit of the suite: '2022-04-22' + Description: null + EDAM operation: + - Annotation + - Standardisation and normalisation + EDAM operation (no superclasses): + - Annotation + - Standardisation and normalisation + EDAM topic: + - Metabolomics + - Compound libraries and screening + - Data submission, annotation and curation + EDAM topic (no superclasses): + - Metabolomics + - Compound libraries and screening + - Data submission, annotation and curation + Galaxy tool ids: + - msmetaenhancer + Galaxy wrapper id: msmetaenhancer + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer + Galaxy wrapper version: 0.4.0 + No. of tool users (5 years) (usegalaxy.eu): 203 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 48 + No. of tool users (5 years) - all main servers: 251 + No. of tool users (all time) (usegalaxy.eu): 203 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 48 + No. of tool users (all time) - all main servers: 251 + Source: https://github.com/RECETOX/MSMetaEnhancer + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 10 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 11 + Tool usage (all time) (usegalaxy.eu): 10 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 11 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Tool for mass spectra metadata annotation. + bio.tool id: msmetaenhancer + bio.tool ids: + - msmetaenhancer + bio.tool name: MSMetaEnhancer +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: matchms + Conda version: 0.27.0 + Date of first commit of the suite: '2022-05-05' + Description: null + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - msp_merge + Galaxy wrapper id: msp_merge + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge + Galaxy wrapper version: 0.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/RECETOX/galaxytools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: lxml + Conda version: null + Date of first commit of the suite: '2023-01-12' + Description: mzML Validator checks if mzML file validates against XML Schema Definition + of HUPO Proteomics Standard Initiative. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - mzml_validator + Galaxy wrapper id: mzml_validator + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator + Galaxy wrapper version: 0.1.0+galaxy2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/RECETOX/galaxytools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + - Proteomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 3 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-10-21' + Description: QCxMS is a quantum chemical (QC) based program that enables users to + calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - qcxms_getres + - qcxms_neutral_run + - qcxms_production_run + Galaxy wrapper id: qcxms + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms + Galaxy wrapper version: 5.2.1 + No. of tool users (5 years) (usegalaxy.eu): 11246 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 11246 + No. of tool users (all time) (usegalaxy.eu): 11246 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 11246 + Source: https://github.com/grimme-lab/QCxMS + Status: To update + Tool usage (5 years) (usegalaxy.eu): 13 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 13 + Tool usage (all time) (usegalaxy.eu): 13 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 13 + ToolShed categories: + - Computational chemistry + - Molecular Dynamics + ToolShed id: QCxMS + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 3 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 3 + UseGalaxy.or: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: click + Conda version: null + Date of first commit of the suite: '2020-12-09' + Description: Execute an SQL statement on a set of tables + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - query + Galaxy wrapper id: query + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/query + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/query + Galaxy wrapper version: '0.2' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Text Manipulation + ToolShed id: query + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 2 + Available on UseGalaxy.org (Main): 2 + Available on UseGalaxy.org.au: 2 + Conda id: r-ramclustr + Conda version: 1.3.1 + Date of first commit of the suite: '2023-05-31' + Description: null + EDAM operation: + - Imputation + - Standardisation and normalisation + - Clustering + - Correlation + EDAM operation (no superclasses): + - Imputation + - Standardisation and normalisation + - Clustering + - Correlation + EDAM topic: + - Metabolomics + EDAM topic (no superclasses): + - Metabolomics + Galaxy tool ids: + - ramclustr + - ramclustr_define_experiment + Galaxy wrapper id: ramclustr + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr + Galaxy wrapper version: 1.3.0 + No. of tool users (5 years) (usegalaxy.eu): 58 + No. of tool users (5 years) (usegalaxy.org): 29 + No. of tool users (5 years) (usegalaxy.org.au): 344 + No. of tool users (5 years) - all main servers: 431 + No. of tool users (all time) (usegalaxy.eu): 58 + No. of tool users (all time) (usegalaxy.org): 29 + No. of tool users (all time) (usegalaxy.org.au): 344 + No. of tool users (all time) - all main servers: 431 + Source: https://rdrr.io/cran/RAMClustR/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 22 + Tool usage (5 years) (usegalaxy.org): 14 + Tool usage (5 years) (usegalaxy.org.au): 4 + Tool usage (5 years) - all main servers: 40 + Tool usage (all time) (usegalaxy.eu): 22 + Tool usage (all time) (usegalaxy.org): 14 + Tool usage (all time) (usegalaxy.org.au): 4 + Tool usage (all time) - all main servers: 40 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 2 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 2 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 2 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 2 + UseGalaxy.eu: 2 + UseGalaxy.fr: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: A feature clustering algorithm for non-targeted mass spectrometric + metabolomics data. + bio.tool id: ramclustr + bio.tool ids: + - ramclustr + bio.tool name: RAMClustR +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: rcx-tk + Conda version: 0.1.0 + Date of first commit of the suite: '2024-08-01' + Description: Tools to process metadata or alkane files. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rcx-tk + Galaxy wrapper id: rcx-tk + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ + Galaxy wrapper version: 0.1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/RECETOX/rcx-tk + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: rcx_tk + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 8 + Available on UseGalaxy.fr: 8 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 8 + Conda id: r-recetox-aplcms + Conda version: 0.13.3 + Date of first commit of the suite: '2023-05-18' + Description: Peak detection tool for HRMS profile data. + EDAM operation: + - Chromatographic alignment + - Quantification + - Peak detection + - Feature extraction + - Alignment + EDAM operation (no superclasses): + - Chromatographic alignment + - Quantification + - Peak detection + - Feature extraction + - Alignment + EDAM topic: + - Metabolomics + EDAM topic (no superclasses): + - Metabolomics + Galaxy tool ids: + - recetox_aplcms_align_features + - recetox_aplcms_compute_clusters + - recetox_aplcms_compute_template + - recetox_aplcms_correct_time + - recetox_aplcms_generate_feature_table + - recetox_aplcms_merge_known_table + - recetox_aplcms_recover_weaker_signals + - recetox_aplcms_remove_noise + Galaxy wrapper id: recetox_aplcms + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms + Galaxy wrapper version: 0.13.3 + No. of tool users (5 years) (usegalaxy.eu): 862 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 48 + No. of tool users (5 years) - all main servers: 910 + No. of tool users (all time) (usegalaxy.eu): 862 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 48 + No. of tool users (all time) - all main servers: 910 + Source: https://github.com/RECETOX/recetox-aplcms + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 12 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 13 + Tool usage (all time) (usegalaxy.eu): 12 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 13 + ToolShed categories: + - Metabolomics + ToolShed id: recetox-aplcms + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 8 + Tools available on UseGalaxy.eu: 8 + Tools available on UseGalaxy.fr: 8 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 8 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 8 + UseGalaxy.eu: 8 + UseGalaxy.fr: 8 + UseGalaxy.or: 8 + biii: null + bio.tool description: recetox-aplcms is a tool for peak detection in mass spectrometry + data. The tool performs (1) noise removal, (2) peak detection, (3) retention time + drift correction, (4) peak alignment and (5) weaker signal recovery as well as + (6) suspect screening. + bio.tool id: recetox-aplcms + bio.tool ids: + - recetox-aplcms + bio.tool name: recetox-aplcms +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: null + Conda version: null + Date of first commit of the suite: '2022-12-02' + Description: null + EDAM operation: + - Annotation + EDAM operation (no superclasses): + - Annotation + EDAM topic: + - Metabolomics + EDAM topic (no superclasses): + - Metabolomics + Galaxy tool ids: + - recetox_msfinder + Galaxy wrapper id: recetox_msfinder + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder + Galaxy wrapper version: v3.5.2 + No. of tool users (5 years) (usegalaxy.eu): 47 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 47 + No. of tool users (all time) (usegalaxy.eu): 47 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 47 + Source: https://github.com/RECETOX/recetox-msfinder + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: This is a modified copy of MS-FINDER with source code modifications + to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation + of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports + molecular formula prediction, metabolie class prediction, and structure elucidation + for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. + bio.tool id: recetox-msfinder + bio.tool ids: + - recetox-msfinder + bio.tool name: recetox-msfinder +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: r-recetox-xmsannotator + Conda version: 0.10.0 + Date of first commit of the suite: '2021-07-21' + Description: null + EDAM operation: + - Expression profile pathway mapping + - Structure comparison + - Isotopic distributions calculation + - Annotation + EDAM operation (no superclasses): + - Expression profile pathway mapping + - Structure comparison + - Isotopic distributions calculation + - Annotation + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - recetox_xmsannotator_advanced + Galaxy wrapper id: recetox_xmsannotator + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator + Galaxy wrapper version: 0.10.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 93 + No. of tool users (5 years) - all main servers: 93 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 93 + No. of tool users (all time) - all main servers: 93 + Source: https://github.com/RECETOX/recetox-xMSannotator + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 2 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 2 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Annotation tool for untargeted LCMS1 data. Uses a database + and adduct list for compound annotation and intensity networks, isotopic patterns + and pathways for annotation scoring. + bio.tool id: recetox-xmsannotator + bio.tool ids: + - recetox-xmsannotator + bio.tool name: recetox-xMSannotator +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: pandas + Conda version: null + Date of first commit of the suite: '2023-11-21' + Description: Removes molecular coordination complexes. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rem_complex + Galaxy wrapper id: rem_complex + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 18 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 18 + No. of tool users (all time) (usegalaxy.eu): 18 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 18 + Source: https://github.com/RECETOX/galaxytools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Metabolomics + ToolShed id: rem_complex + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: pandas + Conda version: null + Date of first commit of the suite: '2024-05-13' + Description: Update column names in an abundance table using a annotation table + with spectral matching results + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rename_annotated_feature + Galaxy wrapper id: rename_annotated_feature + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature + Galaxy wrapper version: 1.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/RECETOX/galaxytools/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: rename_annotated_feature + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2020-09-07' + Description: null + EDAM operation: + - Retention time prediction + - Spectrum calculation + - Deisotoping + - Formatting + - Deposition + EDAM operation (no superclasses): + - Retention time prediction + - Spectrum calculation + - Deisotoping + - Formatting + - Deposition + EDAM topic: + - Metabolomics + - Proteomics experiment + - Machine learning + - Cheminformatics + - Chemistry + EDAM topic (no superclasses): + - Metabolomics + - Proteomics experiment + - Machine learning + - Cheminformatics + - Chemistry + Galaxy tool ids: + - retip_apply + - retip_descriptors + - retip_filter_rt + - retip_train + Galaxy wrapper id: retip + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/retip + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/retip + Galaxy wrapper version: 0.5.4 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/PaoloBnn/Retip + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: 'Retention Time Prediction for Compound Annotation in Untargeted + Metabolomics.Retip is an R package for predicting Retention Time (RT) for small + molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip + - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction + for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, + Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 + 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.' + bio.tool id: retip + bio.tool ids: + - retip + bio.tool name: Retip +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 2 + Conda id: riassigner + Conda version: 0.4.1 + Date of first commit of the suite: '2021-08-19' + Description: null + EDAM operation: + - Standardisation and normalisation + EDAM operation (no superclasses): + - Standardisation and normalisation + EDAM topic: + - Metabolomics + - Compound libraries and screening + - Data submission, annotation and curation + EDAM topic (no superclasses): + - Metabolomics + - Compound libraries and screening + - Data submission, annotation and curation + Galaxy tool ids: + - riassigner + - riassigner_from_comment + Galaxy wrapper id: riassigner + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner + Galaxy wrapper version: 0.4.1 + No. of tool users (5 years) (usegalaxy.eu): 46 + No. of tool users (5 years) (usegalaxy.org): 15 + No. of tool users (5 years) (usegalaxy.org.au): 1 + No. of tool users (5 years) - all main servers: 62 + No. of tool users (all time) (usegalaxy.eu): 46 + No. of tool users (all time) (usegalaxy.org): 15 + No. of tool users (all time) (usegalaxy.org.au): 1 + No. of tool users (all time) - all main servers: 62 + Source: https://github.com/RECETOX/RIAssigner + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 19 + Tool usage (5 years) (usegalaxy.org): 4 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 24 + Tool usage (all time) (usegalaxy.eu): 19 + Tool usage (all time) (usegalaxy.org): 4 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 24 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 2 + UseGalaxy.fr: 1 + UseGalaxy.or: 2 + biii: null + bio.tool description: RIAssigner is a python tool for retention index (RI) computation + for GC-MS data. + bio.tool id: riassigner + bio.tool ids: + - riassigner + bio.tool name: RIAssigner +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: python + Conda version: null + Date of first commit of the suite: '2021-02-25' + Description: RMassBank is an R package for processing tandem MS files and building + of MassBank records. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - rmassbank + Galaxy wrapper id: rmassbank + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank + Galaxy wrapper version: 3.0.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 48 + No. of tool users (5 years) - all main servers: 48 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 48 + No. of tool users (all time) - all main servers: 48 + Source: https://github.com/MassBank/RMassBank + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 1 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 1 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Metabolomics + ToolShed id: rmassbank + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 2 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 2 + Conda id: spec2vec + Conda version: 0.8.0 + Date of first commit of the suite: '2022-12-07' + Description: Mass spectra similarity scoring using a trained Spec2Vec model. + EDAM operation: + - Spectrum calculation + - Spectral library search + - Database search + - Natural product identification + EDAM operation (no superclasses): + - Spectrum calculation + - Spectral library search + - Database search + - Natural product identification + EDAM topic: + - Proteomics experiment + - Metabolomics + - Natural language processing + - Proteomics + EDAM topic (no superclasses): + - Proteomics experiment + - Metabolomics + - Natural language processing + - Proteomics + Galaxy tool ids: + - spec2vec_similarity + - spec2vec_training + Galaxy wrapper id: spec2vec + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec + Galaxy wrapper version: 0.8.0 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1 + Source: https://github.com/iomega/spec2vec + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Metabolomics + ToolShed id: spec2vec + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 2 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 2 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 2 + UseGalaxy.or: 2 + biii: null + bio.tool description: Improved mass spectral similarity scoring through learning + of structural relationships.Spec2vec is a novel spectral similarity score inspired + by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns + relationships between words in sentences, spec2vec does so for mass fragments + and neutral losses in MS/MS spectra. The spectral similarity score is based on + spectral embeddings learnt from the fragmental relationships within a large set + of spectral data.Analysis and benchmarking of mass spectra similarity measures + using gnps data set. + bio.tool id: spec2vec + bio.tool ids: + - spec2vec + bio.tool name: Spec2Vec +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 1 + Available on UseGalaxy.org.au: 1 + Conda id: r-recetox-waveica + Conda version: 0.2.0 + Date of first commit of the suite: '2022-09-19' + Description: Removal of batch effects for large-scale untargeted metabolomics data + based on wavelet analysis. + EDAM operation: + - Standardisation and normalisation + EDAM operation (no superclasses): + - Standardisation and normalisation + EDAM topic: + - Metabolomics + EDAM topic (no superclasses): + - Metabolomics + Galaxy tool ids: + - waveica + Galaxy wrapper id: waveica + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/waveica + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/waveica + Galaxy wrapper version: 0.2.0 + No. of tool users (5 years) (usegalaxy.eu): 39 + No. of tool users (5 years) (usegalaxy.org): 4 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 43 + No. of tool users (all time) (usegalaxy.eu): 39 + No. of tool users (all time) (usegalaxy.org): 4 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 43 + Source: https://github.com/RECETOX/WaveICA + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 3 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 9 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 3 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 9 + ToolShed categories: + - Metabolomics + ToolShed id: null + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 1 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: Removal of batch effects for large-scale untargeted metabolomics + data based on wavelet transform. + bio.tool id: waveica + bio.tool ids: + - waveica + bio.tool name: WaveICA +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 1 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 1 + Conda id: xtb + Conda version: null + Date of first commit of the suite: '2023-09-06' + Description: Performs semiempirical molecular optimization. + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - xtb_molecular_optimization + Galaxy wrapper id: xtb + Galaxy wrapper owner: recetox + Galaxy wrapper parsed folder: https://github.com/RECETOX/galaxytools/tree/master/tools/xtb + Galaxy wrapper source: https://github.com/RECETOX/galaxytools/tree/master/tools/xtb + Galaxy wrapper version: 6.6.1 + No. of tool users (5 years) (usegalaxy.eu): 143 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 143 + No. of tool users (all time) (usegalaxy.eu): 143 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 143 + Source: https://github.com/grimme-lab/xtb + Status: To update + Tool usage (5 years) (usegalaxy.eu): 4 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 4 + Tool usage (all time) (usegalaxy.eu): 4 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 4 + ToolShed categories: + - Metabolomics + ToolShed id: xtb_molecular_optimization + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 1 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 1 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.or: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: snvphyl-tools + Conda version: 1.8.2 + Date of first commit of the suite: '2015-11-26' + Description: Combines freebayes and mpileup files for use by vcf2snvalignment + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - consolidate_vcfs + Galaxy wrapper id: consolidate_vcfs + Galaxy wrapper owner: nml + Galaxy wrapper parsed folder: https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs + Galaxy wrapper source: https://github.com/phac-nml/snvphyl-galaxy + Galaxy wrapper version: 1.8.2 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://snvphyl.readthedocs.io/en/latest/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - 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Taxonomic classification + EDAM operation (no superclasses): + - Taxonomic classification + EDAM topic: + - Metagenomics + - Microbial ecology + - Taxonomy + - Evolutionary biology + - Sequencing + EDAM topic (no superclasses): + - Metagenomics + - Microbial ecology + - Taxonomy + - Evolutionary biology + - Sequencing + Galaxy tool ids: + - FROGS_affiliation_filters + - FROGS_affiliation_postprocess + - FROGS_affiliation_stats + - FROGS_biom_to_stdBiom + - FROGS_biom_to_tsv + - FROGS_cluster_filters + - FROGS_cluster_stats + - FROGS_clustering + - FROGS_demultiplex + - FROGSSTAT_DESeq2_Preprocess + - FROGSSTAT_DESeq2_Visualisation + - FROGSFUNC_step2_functions + - FROGSFUNC_step3_pathways + - FROGSFUNC_step1_placeseqs + - FROGS_itsx + - FROGS_normalisation + - FROGSSTAT_Phyloseq_Alpha_Diversity + - FROGSSTAT_Phyloseq_Beta_Diversity + - FROGSSTAT_Phyloseq_Sample_Clustering + - FROGSSTAT_Phyloseq_Composition_Visualisation + - FROGSSTAT_Phyloseq_Import_Data + - FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance + - FROGSSTAT_Phyloseq_Structure_Visualisation + - FROGS_preprocess + - FROGS_remove_chimera + - FROGS_taxonomic_affiliation + - FROGS_Tree + - FROGS_tsv_to_biom + Galaxy wrapper id: frogs + Galaxy wrapper owner: frogs + Galaxy wrapper parsed folder: https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs + Galaxy wrapper source: https://github.com/geraldinepascal/FROGS-wrappers/ + Galaxy wrapper version: 4.1.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: http://frogs.toulouse.inrae.fr/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: frogs + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 18 + Tools available on GalaxyTrakr: 18 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 28 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.fr: 18 + biii: null + bio.tool description: The user-friendly and Galaxy-supported pipeline FROGS analyses + large sets of DNA amplicons sequences accurately and rapidly, essential for microbe + community studies. + bio.tool id: frogs + bio.tool ids: + - frogs + bio.tool name: FROGS +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: checkv + Conda version: 1.0.3 + Date of first commit of the suite: '2024-09-13' + Description: Assess quality of single-contig viral genomes + EDAM operation: + - Sequence assembly + - Validation + - Read mapping + EDAM operation (no superclasses): + - Sequence assembly + - Validation + - Read mapping + EDAM topic: + - Metagenomics + - Sequence assembly + - Metagenomic sequencing + - Mapping + EDAM topic (no superclasses): + - Metagenomics + - Sequence assembly + - Metagenomic sequencing + - Mapping + Galaxy tool ids: + - checkv_end_to_end + Galaxy wrapper id: checkv + Galaxy wrapper owner: ufz + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv + Galaxy wrapper source: https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ + Galaxy wrapper version: 1.0.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://bitbucket.org/berkeleylab/checkv/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: checkv + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: CheckV is a fully automated command-line pipeline for assessing + the quality of single-contig viral genomes, including identification of host contamination + for integrated proviruses, estimating completeness for genome fragments, and identification + of closed genomes. + bio.tool id: checkv + bio.tool ids: + - checkv + bio.tool name: CheckV +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: genomad + Conda version: 1.8.1 + Date of first commit of the suite: '2024-06-17' + Description: Identify virus and plasmid genomes from nucleotide sequences + EDAM operation: + - Sequence annotation + - Taxonomic classification + EDAM operation (no superclasses): + - Sequence annotation + - Taxonomic classification + EDAM topic: + - Sequence analysis + EDAM topic (no superclasses): + - Sequence analysis + Galaxy tool ids: + - genomad_end_to_end + Galaxy wrapper id: genomad + Galaxy wrapper owner: ufz + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad + Galaxy wrapper source: https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ + Galaxy wrapper version: 1.8.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/apcamargo/genomad/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: genomad + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: geNomad is a tool that identifies virus and plasmid genomes + from nucleotide sequences. It provides state-of-the-art classification performance + and can be used to quickly find mobile genetic elements from genomes, metagenomes, + or metatranscriptomes. + bio.tool id: genomad + bio.tool ids: + - genomad + bio.tool name: geNomad +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: iphop + Conda version: 1.3.3 + Date of first commit of the suite: '2024-10-14' + Description: Integrated Phage Host Prediction + EDAM operation: + - Sample comparison + EDAM operation (no superclasses): + - Sample comparison + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - iphop_predict + Galaxy wrapper id: iphop + Galaxy wrapper owner: ufz + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop + Galaxy wrapper source: https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ + Galaxy wrapper version: 1.3.3 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://bitbucket.org/srouxjgi/iphop/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: iphop + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: An automated command-line pipeline for predicting host genus + of novel bacteriophages and archaeoviruses based on their genome sequences. + bio.tool id: iphop + bio.tool ids: + - iphop + bio.tool name: iPHoP +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2018-06-01' + Description: obtain longest ORF in six-frame translations + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - longORF + Galaxy wrapper id: longorf + Galaxy wrapper owner: mbernt + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf + Galaxy wrapper source: https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ + Galaxy wrapper version: 0.3.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Sequence Analysis + ToolShed id: longorf + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: omero-py + Conda version: 5.11.1 + Date of first commit of the suite: '2024-07-29' + Description: Import images, region of interest, metadata into an OMERO.server using + omero-py + EDAM operation: + - Image analysis + EDAM operation (no superclasses): + - Image analysis + EDAM topic: + - Imaging + - Data visualisation + EDAM topic (no superclasses): + - Imaging + - Data visualisation + Galaxy tool ids: + - omero_import + - omero_metadata_import + - omero_roi_import + Galaxy wrapper id: omero + Galaxy wrapper owner: ufz + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero + Galaxy wrapper source: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero + Galaxy wrapper version: 5.18.0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/ome/omero-py/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Imaging + ToolShed id: omero_upload + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: Client-server Java software for visualisation, management + and analysis of biological microscope images. + bio.tool id: omero + bio.tool ids: + - omero + bio.tool name: OMERO +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: null + Conda version: null + Date of first commit of the suite: '2023-07-29' + Description: suite_scripting + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - singularity_scriptrunner + Galaxy wrapper id: scripting + Galaxy wrapper owner: mbernt + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting + Galaxy wrapper source: https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ + Galaxy wrapper version: '0.1' + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Text Manipulation + ToolShed id: scripting tools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: pandas + Conda version: null + Date of first commit of the suite: '2024-03-25' + Description: Toxicity prediction using QSAR models + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - tt_baseline + Galaxy wrapper id: baseline_calculator + Galaxy wrapper owner: mbernt + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator + Galaxy wrapper source: https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator + Galaxy wrapper version: 0.1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bernt-matthias/mb-galaxy-tools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Ecology + - Text Manipulation + ToolShed id: baseline_toxicity_calculator + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 0 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: r-drc + Conda version: '3.0_1' + Date of first commit of the suite: '2024-04-06' + Description: A tool for analyzing and visualizing the relationship between various + doses and their corresponding biological responses + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - dr_curve + Galaxy wrapper id: dose_responses + Galaxy wrapper owner: ufz + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses + Galaxy wrapper source: https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator + Galaxy wrapper version: 3.0.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/bernt-matthias/mb-galaxy-tools + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Ecology + ToolShed id: dose_response_analysis_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 0 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: {} + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: vibrant + Conda version: 1.2.1 + Date of first commit of the suite: '2024-09-11' + Description: Virus Identification By iteRative ANnoTation + EDAM operation: + - Sequence trimming + - Scaffolding + - Genome annotation + EDAM operation (no superclasses): + - Sequence trimming + - Scaffolding + - Genome annotation + EDAM topic: + - Metagenomics + - Microbial ecology + - Sequence assembly + - Molecular interactions, pathways and networks + - Endocrinology and metabolism + EDAM topic (no superclasses): + - Metagenomics + - Microbial ecology + - Sequence assembly + - Molecular interactions, pathways and networks + - Endocrinology and metabolism + Galaxy tool ids: + - vibrant + Galaxy wrapper id: vibrant + Galaxy wrapper owner: ufz + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant + Galaxy wrapper source: https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant + Galaxy wrapper version: 1.2.1 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/AnantharamanLab/VIBRANT + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: vibrant + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: 'Automated recovery, annotation and curation of microbial + viruses, and evaluation of virome function from genomic sequences.Virus Identification + By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, + last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing + our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: + Automated recovery, annotation and curation of microbial viruses, and evaluation + of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for + automated recovery and annotation of bacterial and archaeal viruses, determination + of genome completeness, and characterization of virome function from metagenomic + assemblies.The QuickStart tutorial provides an introduction to basic DE functionality + and navigation.Please work through the tutorial and use the intercom button on + the bottom right of this page if you have any questions' + bio.tool id: VIBRANT + bio.tool ids: + - VIBRANT + bio.tool name: VIBRANT +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: virsorter + Conda version: 2.2.4 + Date of first commit of the suite: '2024-06-20' + Description: VirSorter2 applies a multi-classifier, expert-guided approach to detect + diverse DNA and RNA virus genomes. + EDAM operation: + - Taxonomic classification + EDAM operation (no superclasses): + - Taxonomic classification + EDAM topic: + - Metagenomics + EDAM topic (no superclasses): + - Metagenomics + Galaxy tool ids: + - virsorter + Galaxy wrapper id: virsorter + Galaxy wrapper owner: ufz + Galaxy wrapper parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter + Galaxy wrapper source: https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter + Galaxy wrapper version: 2.2.4 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: https://github.com/jiarong/VirSorter2/ + Status: Up-to-date + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Metagenomics + ToolShed id: virsorter + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: Identify DNA and RNA virus sequences. + bio.tool id: virsorter + bio.tool ids: + - virsorter + bio.tool name: virsorter +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: astropy + Conda version: null + Date of first commit of the suite: '2023-08-26' + Description: Astronomical archives tools contains tools for querying and fetching + resources from astronomical archives into Galaxy + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - astronomical_archives + Galaxy wrapper id: pyvo_integration + Galaxy wrapper owner: astroteam + Galaxy wrapper parsed folder: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration + Galaxy wrapper source: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ + Galaxy wrapper version: 0.10.0 + No. of tool users (5 years) (usegalaxy.eu): 53 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 53 + No. of tool users (all time) (usegalaxy.eu): 53 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 53 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 6 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 6 + Tool usage (all time) (usegalaxy.eu): 6 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 6 + ToolShed categories: + - Data Source + ToolShed id: astronomicalarchivestool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 1 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 3 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: astropy + Conda version: null + Date of first commit of the suite: '2023-04-11' + Description: AstropyTools library contains Galaxy tools for elementary Astrophysical + operations + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - astropy_fits2bitmap + - astropy_fits2csv + - astropy_fitsinfo + Galaxy wrapper id: astropytools + Galaxy wrapper owner: volodymyrss + Galaxy wrapper parsed folder: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools + Galaxy wrapper source: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools + Galaxy wrapper version: 0.1.0+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 13 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 13 + No. of tool users (all time) (usegalaxy.eu): 13 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 13 + Source: https://github.com/astropy/astropy + Status: To update + Tool usage (5 years) (usegalaxy.eu): 5 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 5 + Tool usage (all time) (usegalaxy.eu): 5 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 5 + ToolShed categories: + - Astronomy + ToolShed id: astropytools + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 3 + Tools available on UseGalaxy.eu: 3 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.cz: 3 + UseGalaxy.eu: 3 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: unzip + Conda version: null + Date of first commit of the suite: '2024-04-19' + Description: Basic simulation of CTA telescope observations using gammapy package + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - cta_astro_tool + Galaxy wrapper id: cta + Galaxy wrapper owner: astroteam + Galaxy wrapper parsed folder: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta + Galaxy wrapper source: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools + Galaxy wrapper version: 0.0.1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 0 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 0 + No. of tool users (all time) (usegalaxy.eu): 0 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 0 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 0 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 0 + Tool usage (all time) (usegalaxy.eu): 0 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 0 + ToolShed categories: + - Astronomy + ToolShed id: cta_astro_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ipython + Conda version: null + Date of first commit of the suite: '2024-02-19' + Description: Basic analysis of Data Level 3 public data sample of HESS gamma-ray + telescope + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - hess_astro_tool + Galaxy wrapper id: hess + Galaxy wrapper owner: astroteam + Galaxy wrapper parsed folder: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess + Galaxy wrapper source: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools + Galaxy wrapper version: 0.0.2+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 1 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 1 + No. of tool users (all time) (usegalaxy.eu): 1 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 1 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 1 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 1 + Tool usage (all time) (usegalaxy.eu): 1 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 1 + ToolShed categories: + - Astronomy + ToolShed id: hess_astro_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null +- Available on UseGalaxy.eu: 1 + Available on UseGalaxy.fr: 0 + Available on UseGalaxy.org (Main): 0 + Available on UseGalaxy.org.au: 0 + Conda id: ipython + Conda version: null + Date of first commit of the suite: '2024-04-17' + Description: SGWB + EDAM operation: [] + EDAM operation (no superclasses): [] + EDAM topic: [] + EDAM topic (no superclasses): [] + Galaxy tool ids: + - sgwb_astro_tool + Galaxy wrapper id: sgwb + Galaxy wrapper owner: astroteam + Galaxy wrapper parsed folder: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb + Galaxy wrapper source: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools + Galaxy wrapper version: 0.0.1+galaxy0 + No. of tool users (5 years) (usegalaxy.eu): 5 + No. of tool users (5 years) (usegalaxy.org): 0 + No. of tool users (5 years) (usegalaxy.org.au): 0 + No. of tool users (5 years) - all main servers: 5 + No. of tool users (all time) (usegalaxy.eu): 5 + No. of tool users (all time) (usegalaxy.org): 0 + No. of tool users (all time) (usegalaxy.org.au): 0 + No. of tool users (all time) - all main servers: 5 + Source: null + Status: To update + Tool usage (5 years) (usegalaxy.eu): 2 + Tool usage (5 years) (usegalaxy.org): 0 + Tool usage (5 years) (usegalaxy.org.au): 0 + Tool usage (5 years) - all main servers: 2 + Tool usage (all time) (usegalaxy.eu): 2 + Tool usage (all time) (usegalaxy.org): 0 + Tool usage (all time) (usegalaxy.org.au): 0 + Tool usage (all time) - all main servers: 2 + ToolShed categories: + - Astronomy + ToolShed id: sgwb_astro_tool + Tools available on APOSTL: 0 + Tools available on ARGs-OAP: 0 + Tools available on CIRM-CFBP: 0 + Tools available on ChemFlow: 0 + Tools available on Coloc-stats: 0 + Tools available on CropGalaxy: 0 + Tools available on Dintor: 0 + Tools available on GASLINI: 0 + Tools available on Galaxy@AuBi: 0 + Tools available on Galaxy@Pasteur: 0 + Tools available on GalaxyTrakr: 0 + Tools available on Genomic Hyperbrowser: 0 + Tools available on GigaGalaxy: 0 + Tools available on HyPhy HIV NGS Tools: 0 + Tools available on IPK Galaxy Blast Suite: 0 + Tools available on ImmPort Galaxy: 0 + Tools available on InteractoMIX: 0 + Tools available on MISSISSIPPI: 0 + Tools available on Mandoiu Lab: 0 + Tools available on MiModD NacreousMap: 0 + Tools available on Oqtans: 0 + Tools available on Palfinder: 0 + Tools available on PepSimili: 0 + Tools available on PhagePromotor: 0 + Tools available on UseGalaxy.be: 0 + Tools available on UseGalaxy.cz: 0 + Tools available on UseGalaxy.eu: 1 + Tools available on UseGalaxy.fr: 0 + Tools available on UseGalaxy.no: 0 + Tools available on UseGalaxy.org (Main): 0 + Tools available on UseGalaxy.org.au: 0 + Tools available on Viral Variant Visualizer (VVV): 0 + availability: + UseGalaxy.eu: 1 + biii: null + bio.tool description: null + bio.tool id: null + bio.tool ids: [] + bio.tool name: null diff --git a/docs/_data/topnav.yml b/docs/_data/topnav.yml new file mode 100644 index 00000000..d600a759 --- /dev/null +++ b/docs/_data/topnav.yml @@ -0,0 +1,12 @@ +## +## if you want to list an external url, use external_url instead of url. the theme will apply a different link base. +subitems: +- title: Tools + url: / +- title: Workflows + url: /workflows +- title: Training + url: /training +- title: About + url: /about + \ No newline at end of file diff --git a/docs/_data/tutorials.yml b/docs/_data/tutorials.yml new file mode 100644 index 00000000..31829070 --- /dev/null +++ b/docs/_data/tutorials.yml @@ -0,0 +1,16194 @@ +admin/advanced-galaxy-customisation: + edam_operation: [] + edam_topic: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: false + mod_date: '2023-04-17' + pageviews: 5997019 + pub_date: '2017-06-27' + short_tools: [] + slides: true + title: Advanced customisation of a Galaxy instance + topic_name_human: Galaxy Server administration + url: https://training.galaxyproject.org//topics/admin/tutorials/advanced-galaxy-customisation/slides.html + version: 18 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 153 + visitors: 2165813 +admin/ansible: + edam_operation: [] + edam_topic: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: true + mod_date: '2024-08-08' + pageviews: 6007714 + 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feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - GalaxyTrakr + - UseGalaxy.cz + - UseGalaxy.no + - UseGalaxy.org (Main) + - UseGalaxy.org.au + mod_date: '2023-11-09' + pageviews: 5531 + pub_date: '2018-03-07' + short_tools: + - mimodd_map + - mimodd_varcall + - mimodd_varextract + - mimodd_vcf_filter + - snpEff + - tp_find_and_replace + - mimodd_varreport + - snpEff_download + slides: false + title: Mapping and molecular identification of phenotype-causing mutations + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html + version: 16 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 178 + visitors: 3634 +variant-analysis/microbial-variants: + edam_operation: + - Genome visualisation + - Variant calling + - Phylogenetic tree generation + - Phylogenetic tree visualisation + edam_topic: + - Genomics + - Sequence assembly + - DNA polymorphism + - Microbiology + - Sequence analysis + - Genetic variation + exact_supported_servers: + - UseGalaxy.be + - UseGalaxy.eu + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - GalaxyTrakr + - UseGalaxy.cz + - UseGalaxy.fr + - UseGalaxy.no + - UseGalaxy.org.au + mod_date: '2024-03-15' + pageviews: 20807 + pub_date: '2018-02-26' + short_tools: + - snippy + - jbrowse + slides: false + title: Microbial Variant Calling + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html + version: 23 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 119 + visitors: 12572 +variant-analysis/non-dip: + edam_operation: + - Sequencing quality control + - Genome indexing + - Sequence alignment analysis + - Sequence composition calculation + - Statistical calculation + - Data handling + - Sequence alignment + - Generation + - Read mapping + - Variant calling + - Formatting + edam_topic: + - Genomics + - Sequence assembly + - DNA polymorphism + - Microbiology + - Sequence analysis + - Genetic variation + exact_supported_servers: + - UseGalaxy.be + - UseGalaxy.eu + - UseGalaxy.fr + - UseGalaxy.no + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - UseGalaxy.cz + - UseGalaxy.org.au + mod_date: '2024-03-15' + pageviews: 13749 + pub_date: '2017-02-16' + short_tools: + - bamleftalign + - picard_MergeSamFiles + - bwa_mem + - bamFilter + - picard_MarkDuplicates + - vcffilter2 + - fastqc + - vcf2tsv + - freebayes + - Cut1 + slides: false + title: Calling variants in non-diploid systems + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html + version: 23 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 128 + visitors: 7247 +variant-analysis/pox-tiled-amplicon: + edam_operation: + - Sequencing quality control + - Genome indexing + - Sequence alignment analysis + - Sequence analysis + - Sequence contamination filtering + - Multiple sequence alignment + - Sequence alignment + - Generation + - Read mapping + - Local alignment + - Global alignment + edam_topic: [] + exact_supported_servers: + - UseGalaxy.eu + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - UseGalaxy.org (Main) + mod_date: '2024-03-20' + pageviews: 724 + pub_date: '2023-05-15' + short_tools: + - bwa_mem + - 'EMBOSS: maskseq51' + - param_value_from_file + - __ZIP_COLLECTION__ + - fasta_compute_length + - ivar_consensus + - fatovcf + - Grep1 + - Cut1 + - __APPLY_RULES__ + - qualimap_bamqc + - ivar_trim + - Add_a_column1 + - fastp + - datamash_ops + - samtools_view + - mimodd_info + - rbc_mafft + - samtools_merge + - fasta_regex_finder + - compose_text_param + - upload1 + slides: false + title: Pox virus genome analysis from tiled-amplicon sequencing data + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html + version: 4 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 178 + visitors: 601 +variant-analysis/sars-cov-2: + edam_operation: + - Sequencing quality control + - Genome indexing + - Sequence contamination filtering + - Data handling + - SNP detection + - Sequence alignment + - Generation + - Validation + - Read mapping + - Formatting + edam_topic: [] + exact_supported_servers: + - UseGalaxy.eu + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - MISSISSIPPI + - UseGalaxy.be + - UseGalaxy.cz + - UseGalaxy.fr + - UseGalaxy.no + - UseGalaxy.org.au + mod_date: '2024-06-14' + pageviews: 18954 + pub_date: '2020-06-24' + short_tools: + - bwa_mem + - snpeff_sars_cov_2 + - lofreq_viterbi + - picard_MarkDuplicates + - snpSift_extractFields + - Grep1 + - multiqc + - samtools_stats + - fastp + - lofreq_indelqual + - Filter1 + - fasterq_dump + - lofreq_call + - tp_cut_tool + slides: false + title: 'From NCBI''s Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis' + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2/tutorial.html + version: 16 + video: false + video_versions: 1 + video_view: 0 + visit_duration: 175 + visitors: 12442 +variant-analysis/sars-cov-2-variant-discovery: + edam_operation: + - Tree-based sequence alignment + - Variant calling + - Variant classification + - Methylation analysis + edam_topic: [] + exact_supported_servers: + - UseGalaxy.eu + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - UseGalaxy.cz + mod_date: '2024-10-01' + pageviews: 12136 + pub_date: '2021-06-30' + short_tools: + - nextclade + - fasta_regex_finder + - pangolin + - datamash_ops + - upload1 + - Filter1 + slides: false + title: Mutation calling, viral genome reconstruction and lineage/clade assignment + from SARS-CoV-2 sequencing data + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html + version: 17 + video: false + video_versions: 3 + video_view: 0 + visit_duration: 208 + visitors: 6555 +variant-analysis/somatic-variant-discovery: + edam_operation: + - Sequencing quality control + - Genome indexing + - Sequence composition calculation + - Copy number estimation + - Statistical calculation + - Sequence alignment + - Genome alignment + - Generation + - Validation + - Sequence visualisation + - Read mapping + - Variant calling + edam_topic: [] + exact_supported_servers: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - UseGalaxy.be + - UseGalaxy.cz + - UseGalaxy.eu + - UseGalaxy.no + - UseGalaxy.org.au + mod_date: '2024-09-19' + pageviews: 1591 + pub_date: '2022-10-05' + short_tools: + - bamleftalign + - samtools_calmd + - circos + - trimmomatic + - bwa_mem + - tp_replace_in_line + - control_freec + - Grep1 + - __EXTRACT_DATASET__ + - __RELABEL_FROM_FILE__ + - tp_text_file_with_recurring_lines + - fastqc + - samtools_rmdup + - multiqc + - samtools_view + - __BUILD_LIST__ + slides: false + title: Somatic Variant Discovery from WES Data Using Control-FREEC + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html + version: 13 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 116 + visitors: 1210 +variant-analysis/somatic-variants: + edam_operation: + - Sequencing quality control + - Genome indexing + - Sequence alignment analysis + - Sequence composition calculation + - Data handling + - Statistical calculation + - Sequence alignment + - Generation + - Validation + - Read mapping + - Variant calling + edam_topic: [] + exact_supported_servers: + - UseGalaxy.be + - UseGalaxy.eu + - UseGalaxy.no + - UseGalaxy.org (Main) + - UseGalaxy.org.au + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - UseGalaxy.cz + - UseGalaxy.fr + mod_date: '2023-11-09' + pageviews: 22174 + pub_date: '2019-03-13' + short_tools: + - bamleftalign + - samtools_calmd + - bg_column_arrange_by_header + - trimmomatic + - bwa_mem + - gemini_load + - bamFilter + - gemini_query + - tp_easyjoin_tool + - samtools_rmdup + - multiqc + - snpEff + - fastqc + - varscan_somatic + - gemini_annotate + slides: false + title: Identification of somatic and germline variants from tumor and normal sample + pairs + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variants/tutorial.html + version: 15 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 150 + visitors: 11789 +variant-analysis/tb-variant-analysis: + edam_operation: + - Sequencing quality control + - Taxonomic classification + - Phylogenetic tree generation + - Sequence alignment analysis + - Sequence contamination filtering + - Sequence analysis + - Sequence composition calculation + - Antimicrobial resistance prediction + - Statistical calculation + - Sequence alignment + - Validation + - Phylogenetic tree visualisation + - Local alignment + - Variant calling + - Global alignment + - Genome visualisation + edam_topic: + - Genomics + - Microbiology + - Sequence assembly + - Genetic variation + - Public health and epidemiology + - Infectious disease + exact_supported_servers: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: [] + mod_date: '2024-07-26' + pageviews: 9224 + pub_date: '2020-07-25' + short_tools: + - tp_awk_tool + - tbvcfreport + - tp_sed_tool + - bcftools_consensus + - tb_profiler_profile + - mosdepth + - multiqc + - samtools_stats + - jvarkit_wgscoverageplotter + - qualimap_bamqc + - tb_variant_filter + - jbrowse + - fastp + - snippy + - __FLATTEN__ + - kraken2 + - 'EMBOSS: seqret84' + - fastqc + - upload1 + - EMBOSS:%20seqret84 + slides: false + title: M. tuberculosis Variant Analysis + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html + version: 30 + video: false + video_versions: 2 + video_view: 0 + visit_duration: 176 + visitors: 5831 +variant-analysis/trio-analysis: + edam_operation: + - Genetic variation analysis + - Sequence analysis + edam_topic: [] + exact_supported_servers: + - UseGalaxy.eu + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - UseGalaxy.cz + - UseGalaxy.org.au + mod_date: '2024-09-17' + pageviews: 2803 + pub_date: '2022-05-19' + short_tools: + - bcftools_norm + - tp_grep_tool + - gemini_load + - gene_iobio_display_generation_iframe + - CONVERTER_gz_to_uncompressed + - pyega3 + - regexColumn1 + - snpEff + - CONVERTER_uncompressed_to_gz + - Filter1 + - bcftools_merge + - gemini_inheritance + slides: false + title: Trio Analysis using Synthetic Datasets from RD-Connect GPAP + topic_name_human: Variant Analysis + url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/trio-analysis/tutorial.html + version: 13 + video: false + video_versions: 1 + video_view: 0 + visit_duration: 240 + visitors: 1438 +visualisation/bad-graphs: + edam_operation: [] + edam_topic: [] + exact_supported_servers: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: false + inexact_supported_servers: + - UseGalaxy.eu + - UseGalaxy.org + - UseGalaxy.org.au + - UseGalaxy.fr + mod_date: '2023-11-20' + pageviews: 1278863 + pub_date: '2023-11-20' + short_tools: [] + slides: true + title: Friends Don't Let Friends Make Bad Graphs + topic_name_human: Visualisation + url: https://training.galaxyproject.org//topics/visualisation/tutorials/bad-graphs/slides.html + version: 2 + video: true + video_versions: 0 + video_view: 0 + visit_duration: 154 + visitors: 524177 +visualisation/circos: + edam_operation: + - Sequence visualisation + edam_topic: [] + exact_supported_servers: + - Galaxy@Pasteur + - MISSISSIPPI + - UseGalaxy.eu + - UseGalaxy.fr + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - UseGalaxy.be + - UseGalaxy.cz + - UseGalaxy.no + mod_date: '2024-10-15' + pageviews: 6039908 + pub_date: '2020-01-10' + short_tools: + - circos + - Grep1 + - random_lines1 + - Remove beginning1 + - upload1 + - Cut1 + slides: true + title: Visualisation with Circos + topic_name_human: Visualisation + url: https://training.galaxyproject.org//topics/visualisation/tutorials/circos/tutorial.html + version: 22 + video: false + video_versions: 1 + video_view: 0 + visit_duration: 257 + visitors: 2191696 +visualisation/circos-microbial: + edam_operation: + - Sequence visualisation + edam_topic: [] + exact_supported_servers: + - UseGalaxy.cz + - UseGalaxy.eu + - UseGalaxy.fr + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - MISSISSIPPI + - UseGalaxy.be + - UseGalaxy.no + - UseGalaxy.org (Main) + - UseGalaxy.org.au + mod_date: '2024-09-17' + pageviews: 951 + pub_date: '2023-11-08' + short_tools: + - circos + - circos_gc_skew + - circos_wiggle_to_scatter + - circos_interval_to_tile + - deeptools_bam_coverage + - gff2bed1 + - circos_interval_to_text + - Cut1 + slides: false + title: Ploting a Microbial Genome with Circos + topic_name_human: Visualisation + url: https://training.galaxyproject.org//topics/visualisation/tutorials/circos-microbial/tutorial.html + version: 3 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 103 + visitors: 741 +visualisation/introduction: + edam_operation: [] + edam_topic: [] + exact_supported_servers: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: false + inexact_supported_servers: + - UseGalaxy.eu + - UseGalaxy.org + - UseGalaxy.org.au + - UseGalaxy.fr + mod_date: '2023-01-12' + pageviews: 5997165 + pub_date: '2020-01-10' + short_tools: [] + slides: true + title: Visualisations in Galaxy + topic_name_human: Visualisation + url: https://training.galaxyproject.org//topics/visualisation/tutorials/introduction/slides.html + version: 1 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 153 + visitors: 2165910 +visualisation/jbrowse: + edam_operation: + - Genome visualisation + edam_topic: [] + exact_supported_servers: + - Galaxy@AuBi + - UseGalaxy.be + - UseGalaxy.eu + - UseGalaxy.fr + - UseGalaxy.no + - UseGalaxy.org (Main) + - UseGalaxy.org.au + feedback_mean_note: null + feedback_number: 0 + hands_on: true + inexact_supported_servers: + - Galaxy@Pasteur + - GalaxyTrakr + - MISSISSIPPI + - UseGalaxy.cz + mod_date: '2024-10-15' + pageviews: 6002555 + pub_date: '2020-01-10' + short_tools: + - jbrowse + slides: true + title: Genomic Data Visualisation with JBrowse + topic_name_human: Visualisation + url: https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html + version: 17 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 287 + visitors: 2169871 diff --git a/docs/_data/workflows.yml b/docs/_data/workflows.yml new file mode 100644 index 00000000..8824f4dc --- /dev/null +++ b/docs/_data/workflows.yml @@ -0,0 +1,141240 @@ +- create_time: '2024-10-18' + creators: + - "Marie Joss\xE9" + doi: null + edam_operation: [] + edam_topic: [] + id: '1182' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/1182?version=1 + name: Ocean's variables 2.0 + number_of_steps: 5 + source: WorkflowHub + tags: + - Earth-system + - Ocean + tools: + - Create a climatology (not interactively) + - Create a climatology interactively with notebooks + - Final step to visualize in different way a ocean variable like the phosphate. + - Interactively subset you data. + update_time: '2024-10-18' + versions: 1 +- create_time: '2024-10-15' + creators: + - Yvan Le Bras + - Daniel Caon (LNE) + doi: 10.48546/workflowhub.workflow.1181.1 + edam_operation: [] + edam_topic: + - Biodiversity + - Ecology + id: '1181' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/1181?version=1 + name: Evaluation IA-Biodiv workflow + number_of_steps: 1 + source: WorkflowHub + tags: + - Evaluation + - IA + tools: + - interactive_tool_jupyter_notebook + update_time: '2024-10-15' + versions: 1 +- create_time: '2024-10-07' + creators: + - Nadolina Brajuka + doi: null + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: '645' + latest_version: 8 + license: BSD-3-Clause + link: https://workflowhub.eu/workflows/645?version=8 + name: Assembly-decontamination-VGP9/main + number_of_steps: 10 + source: WorkflowHub + tags: [] + tools: + - Cut1 + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - ncbi_blastn_wrapper + - parse_mito_blast + - Filter1 + update_time: '2024-10-13' + versions: 8 +- create_time: '2024-10-07' + creators: + - VGP + - ' Galaxy' + doi: null + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: '625' + latest_version: 12 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/625?version=12 + name: Scaffolding-HiC-VGP8/main + number_of_steps: 30 + source: WorkflowHub + tags: [] + tools: + - bwa_mem2 + - '' + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - compose_text_param + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-10-07' + versions: 12 +- create_time: '2024-10-07' + creators: + - GalaxyP + doi: null + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: '1177' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/1177?version=1 + name: clinicalmp-quantitation/main + number_of_steps: 7 + source: WorkflowHub + tags: [] + tools: + - maxquant + - 'extracting microbial Peptides + + Grep1' + - 'Quantified-Peptides + + Grouping1' + - 'extract proteins + + Cut1' + - 'Quantified-Proteins + + Grouping1' + - 'extract peptides + + Cut1' + - 'extracting microbial Proteins + + Grep1' + update_time: '2024-10-07' + versions: 1 +- create_time: '2024-10-07' + creators: + - Peter van Heusden + doi: null + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '155' + latest_version: 5 + license: MIT + link: https://workflowhub.eu/workflows/155?version=5 + name: sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE + number_of_steps: 16 + source: WorkflowHub + tags: [] + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2024-10-07' + versions: 5 +- create_time: '2024-10-07' + creators: + - Wolfgang Maier + doi: null + edam_operation: [] + edam_topic: [] + id: '109' + latest_version: 9 + license: MIT + link: https://workflowhub.eu/workflows/109?version=9 + name: sars-cov-2-variation-reporting/COVID-19-VARIATION-REPORTING + number_of_steps: 30 + source: WorkflowHub + tags: [] + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2024-10-07' + versions: 9 +- create_time: '2024-10-07' + creators: + - Wolfgang Maier + doi: null + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '110' + latest_version: 10 + license: MIT + link: https://workflowhub.eu/workflows/110?version=10 + name: sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA + number_of_steps: 25 + source: WorkflowHub + tags: + - ARTIC + - BY-COVID + - covid-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - "\n __FILTER_FAILED_DATASETS__" + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - "\n __FLATTEN__" + - lofreq_filter + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-10-07' + versions: 10 +- create_time: '2024-10-07' + creators: + - Abromics None + - Pierre Marin + - Clea Siguret + doi: null + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: '1043' + latest_version: 5 + license: GPL-3.0-or-later + link: https://workflowhub.eu/workflows/1043?version=5 + name: bacterial-genome-assembly/main + number_of_steps: 7 + source: WorkflowHub + tags: + - ABRomics + - Assembly + - FASTQ + - Genomics + - bacterial-genomics + - paired-end + - quality + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-10-07' + versions: 5 +- create_time: '2024-10-12' + creators: + - ABRomics None + - Pierre Marin + - Clea Siguret + doi: null + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: '1052' + latest_version: 6 + license: GPL-3.0-or-later + link: https://workflowhub.eu/workflows/1052?version=6 + name: quality-and-contamination-control/main + number_of_steps: 6 + source: WorkflowHub + tags: + - ABRomics + - FASTQ + - Genomics + - bacterial-genomics + - paired-end + - quality + - taxonomy-assignment + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-10-12' + versions: 6 +- create_time: '2024-09-24' + creators: + - Diego De Panis + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '1164' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1164?version=1 + name: ERGA HiC Pri Scaffolding+QC YaHS v2409 (WF4) + number_of_steps: 17 + source: WorkflowHub + tags: + - Assembly + - ERGA + - HiC + - QC + tools: + - bwa_mem2 + - yahs + - merqury + - pretext_snapshot + - gfastats + - pretext_map + - gfa_to_fa + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-24' + versions: 1 +- create_time: '2024-09-24' + creators: + - Diego De Panis + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '1163' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1163?version=1 + name: ERGA HiFi PriAlt Purge+QC v2409 (WF3) + number_of_steps: 25 + source: WorkflowHub + tags: + - Assembly + - ERGA + - HiFi + - QC + tools: + - merqury + - gfastats + - cat1 + - gfa_to_fa + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-24' + versions: 1 +- create_time: '2024-09-24' + creators: + - Diego De Panis + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Transcriptome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '1162' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1162?version=1 + name: ERGA HiFi-only Assembly+QC Hifiasm v2409 (WF2) + number_of_steps: 12 + source: WorkflowHub + tags: + - Assembly + - ERGA + - HiFi + - QC + tools: + - hifiasm + - merqury + - gfastats + - gfa_to_fa + - bandage_image + - param_value_from_file + - busco + update_time: '2024-09-24' + versions: 1 +- create_time: '2024-09-18' + creators: + - Diego De Panis + doi: null + edam_operation: + - Sequence trimming + - k-mer counting + - Genotyping + edam_topic: + - Whole genome sequencing + id: '603' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/603?version=2 + name: ERGA Profiling HiFi v2409 (WF1) + number_of_steps: 17 + source: WorkflowHub + tags: + - ERGA + - HiFi + - Profiling + tools: + - Cut1 + - genomescope + - Add_a_column1 + - tp_grep_tool + - tp_cut_tool + - smudgeplot + - Convert characters1 + - tp_find_and_replace + - meryl + - param_value_from_file + update_time: '2024-09-18' + versions: 2 +- create_time: '2024-09-18' + creators: + - Diego De Panis + doi: null + edam_operation: + - Statistical calculation + - Sequence conversion + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - DNA transcription + - Read pre-processing + - DNA translation + - Sequencing quality control + edam_topic: + - Whole genome sequencing + id: '602' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/602?version=2 + name: ERGA DataQC HiFi v2409 (WF0) + number_of_steps: 5 + source: WorkflowHub + tags: + - DataQC + - ERGA + - HiFi + tools: + - fastqc + - collapse_dataset + - cutadapt + - seqkit_stats + - multiqc + update_time: '2024-09-18' + versions: 2 +- create_time: '2024-09-18' + creators: + - Diego De Panis + doi: null + edam_operation: + - Statistical calculation + - Sequence conversion + - Sequence composition calculation + - Validation + - Sequence contamination filtering + - Sequence trimming + - DNA transcription + - DNA translation + - Sequencing quality control + edam_topic: + - Whole genome sequencing + id: '601' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/601?version=2 + name: ERGA DataQC Illumina v2409 (WF0) + number_of_steps: 7 + source: WorkflowHub + tags: + - DataQC + - ERGA + - illumina + tools: + - fastqc + - fastp + - collapse_dataset + - __FLATTEN__ + - seqkit_stats + - multiqc + update_time: '2024-09-18' + versions: 2 +- create_time: '2022-11-24' + creators: [] + doi: null + edam_operation: + - Parsing + - Data handling + - Genome assembly + - Genome indexing + - Genome alignment + - Read mapping + - Read binning + - Sequence contamination filtering + - Sequence trimming + - RNA-Seq analysis + - Antimicrobial resistance prediction + - Sequence alignment + - Multilocus sequence typing + edam_topic: [] + id: '407' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/407?version=1 + name: 'Workflow 3: AMR - SeqSero2/SISTR' + number_of_steps: 14 + source: WorkflowHub + tags: + - Bioinformatics + - antimicrobial resistance + tools: + - mob_recon + - bbtools_bbduk + - srst2 + - kma_map + - __UNZIP_COLLECTION__ + - bbtools_tadpole + - shovill + - hamronize_summarize + - sistr_cmd + - hamronize_tool + - seqsero2 + update_time: '2024-09-09' + versions: 1 +- create_time: '2023-11-07' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '644' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/644?version=1 + name: 'Workflow 2: Sciensano' + number_of_steps: 1 + source: WorkflowHub + tags: [] + tools: + - pipeline_stec_1.0 + update_time: '2024-09-09' + versions: 1 +- create_time: '2023-05-11' + creators: [] + doi: null + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + - Genome assembly + edam_topic: [] + id: '470' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/470?version=1 + name: 'Workflow 4: Staramr' + number_of_steps: 10 + source: WorkflowHub + tags: + - 10.3390/microorganisms10020292 + - AMR + - AMR-detection + - Bioinformatics + - antimicrobial resistance + tools: + - staramr_search + - abricate + - collapse_dataset + - shovill + - hamronize_summarize + - tp_find_and_replace + - hamronize_tool + update_time: '2024-09-09' + versions: 1 +- create_time: '2023-10-31' + creators: [] + doi: null + edam_operation: + - Antimicrobial resistance prediction + edam_topic: [] + id: '634' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/634?version=1 + name: 'Workflow 1: AbritAMR' + number_of_steps: 1 + source: WorkflowHub + tags: [] + tools: + - abritamr + update_time: '2024-09-09' + versions: 1 +- create_time: '2024-09-03' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.1114.1 + edam_operation: + - Statistical calculation + - Genome assembly + - De-novo assembly + - Sequence composition calculation + - Cross-assembly + - Mapping assembly + - Sequence assembly visualisation + - Sequencing quality control + edam_topic: [] + id: '1114' + latest_version: 1 + license: GPL-3.0-or-later + link: https://workflowhub.eu/workflows/1114?version=1 + name: Genome assembly workflow for nanopore reads, for TSI + number_of_steps: 10 + source: WorkflowHub + tags: + - TSI + - genome_assembly + - nanopore + tools: + - fastqc + - split_file_to_collection + - collapse_dataset + - flye + - bandage_info + - fasta-stats + - porechop + - bandage_image + - nanofilt + update_time: '2024-09-03' + versions: 1 +- create_time: '2024-09-02' + creators: + - "Marie Joss\xE9" + doi: null + edam_operation: [] + edam_topic: [] + id: '1113' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/1113?version=1 + name: Full Analyse Argo data + number_of_steps: 10 + source: WorkflowHub + tags: + - Earth-system + - Ocean + - pangeo + tools: [] + update_time: '2024-09-02' + versions: 1 +- create_time: '2024-08-21' + creators: + - "Marie Joss\xE9" + doi: null + edam_operation: [] + edam_topic: + - Marine biology + id: '1105' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/1105?version=1 + name: Marine Omics identifying biosynthetic gene clusters + number_of_steps: 5 + source: WorkflowHub + tags: + - Earth-system + - Marine omics + - Ocean + tools: + - Create the protein fasta file + - Create TSV file for Sanntis + - Use of Sanntis + - Remove useless * in the protein fasta file + update_time: '2024-08-21' + versions: 1 +- create_time: '2024-08-09' + creators: + - Diego De Panis + doi: 10.48546/workflowhub.workflow.1096.1 + edam_operation: + - Data handling + - Genome assembly + - Scaffolding + - Genome annotation + - Transcriptome assembly + - Differential protein expression profiling + - Sequence assembly validation + edam_topic: + - Genomics + id: '1096' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1096?version=1 + name: ERGA-BGE Genome Report ANNOT analyses + number_of_steps: 11 + source: WorkflowHub + tags: + - Annotation + - ERGA + - Genomics + - QC + tools: + - tp_text_file_with_recurring_lines + - collapse_dataset + - lftp + - agat + - omark + - busco + update_time: '2024-08-26' + versions: 1 +- create_time: '2024-08-20' + creators: + - Diego De Panis + doi: 10.48546/workflowhub.workflow.1104.1 + edam_operation: + - Sequence database search + - Sequence alignment analysis + - De-novo assembly + - Primer removal + - Pairwise sequence alignment + - Sequence assembly validation + - Sequencing quality control + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Sequence contamination filtering + - Sequence trimming + - Transcriptome assembly + - Data retrieval + - Read pre-processing + - Sequence alignment + - Genotyping + edam_topic: + - Genomics + id: '1104' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1104?version=1 + name: ERGA-BGE Genome Report ASM analyses (one-asm HiFi + HiC) + number_of_steps: 45 + source: WorkflowHub + tags: + - Genome assembly + - Genomics + - QC + tools: + - hicexplorer_hicmergematrixbins + - tp_text_file_with_recurring_lines + - __EXTRACT_DATASET__ + - collapse_dataset + - genomescope + - fasterq_dump + - lftp + - pairtools_dedup + - bedtools_makewindowsbed + - pairtools_sort + - hicexplorer_hicplotmatrix + - gfastats + - cutadapt + - __FLATTEN__ + - fastp + - blobtoolkit + - CONVERTER_fasta_to_fai + - smudgeplot + - bg_diamond + - minimap2 + - meryl + - pick_value + - pairtools_parse + - pairtools_split + - bwa_mem2 + - sam_merge2 + - sambamba_flagstat + - Cut1 + - cooler_cload_tabix + - merqury + - sambamba_merge + - rseqc_bam_stat + - datasets_download_genome + - cooler_csort_tabix + - busco + update_time: '2024-08-20' + versions: 1 +- create_time: '2024-08-19' + creators: + - Diego De Panis + doi: 10.48546/workflowhub.workflow.1103.2 + edam_operation: + - Sequence database search + - Sequence alignment analysis + - De-novo assembly + - Sequence assembly validation + - Sequencing quality control + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Sequence contamination filtering + - Sequence trimming + - Transcriptome assembly + - Data retrieval + - Sequence alignment + - Genotyping + edam_topic: + - Genomics + id: '1103' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/1103?version=2 + name: ERGA-BGE Genome Report ASM analyses (one-asm WGS Illumina PE + HiC) + number_of_steps: 45 + source: WorkflowHub + tags: + - Genome assembly + - Genomics + - QC + tools: + - hicexplorer_hicmergematrixbins + - tp_text_file_with_recurring_lines + - __EXTRACT_DATASET__ + - collapse_dataset + - genomescope + - fasterq_dump + - lftp + - pairtools_dedup + - bedtools_makewindowsbed + - pairtools_sort + - hicexplorer_hicplotmatrix + - gfastats + - __FLATTEN__ + - fastp + - blobtoolkit + - CONVERTER_fasta_to_fai + - smudgeplot + - bg_diamond + - meryl + - pick_value + - pairtools_parse + - pairtools_split + - bwa_mem2 + - sam_merge2 + - sambamba_flagstat + - Cut1 + - cooler_cload_tabix + - merqury + - sambamba_merge + - rseqc_bam_stat + - datasets_download_genome + - cooler_csort_tabix + - busco + update_time: '2024-08-20' + versions: 2 +- create_time: '2024-10-07' + creators: + - Galaxy + - ' VGP' + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: '633' + latest_version: 13 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/633?version=13 + name: Purge-duplicate-contigs-VGP6/main + number_of_steps: 43 + source: WorkflowHub + tags: [] + tools: + - '' + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_cut_tool + - cat1 + - tp_awk_tool + - compose_text_param + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-10-07' + versions: 13 +- create_time: '2024-10-07' + creators: + - Galaxy + - ' VGP' + doi: null + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: '643' + latest_version: 5 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/643?version=5 + name: Scaffolding-Bionano-VGP7/main + number_of_steps: 13 + source: WorkflowHub + tags: [] + tools: + - '' + - Cut1 + - gfastats + - tp_find_and_replace + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-10-13' + versions: 5 +- create_time: '2024-10-07' + creators: + - Galaxy + - ' VGP' + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: '751' + latest_version: 7 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/751?version=7 + name: Purge-duplicates-one-haplotype-VGP6b/main + number_of_steps: 34 + source: WorkflowHub + tags: [] + tools: + - '' + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_grep_tool + - tp_cut_tool + - tp_awk_tool + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-10-13' + versions: 7 +- create_time: '2024-10-07' + creators: + - Galaxy + - ' VGP' + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: '612' + latest_version: 11 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/612?version=11 + name: Assembly-Hifi-only-VGP3/main + number_of_steps: 37 + source: WorkflowHub + tags: [] + tools: + - '' + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-10-13' + versions: 11 +- create_time: '2024-10-07' + creators: + - Galaxy + - ' VGP' + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: '642' + latest_version: 9 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/642?version=9 + name: Assembly-Hifi-Trio-phasing-VGP5/main + number_of_steps: 38 + source: WorkflowHub + tags: [] + tools: + - '' + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-10-07' + versions: 9 +- create_time: '2024-10-07' + creators: + - VGP + - ' Galaxy' + doi: null + edam_operation: [] + edam_topic: [] + id: '631' + latest_version: 4 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/631?version=4 + name: kmer-profiling-hifi-trio-VGP2/main + number_of_steps: 10 + source: WorkflowHub + tags: [] + tools: + - meryl + - genomescope + update_time: '2024-10-13' + versions: 4 +- create_time: '2024-10-07' + creators: + - VGP + - ' Galaxy' + doi: null + edam_operation: [] + edam_topic: [] + id: '632' + latest_version: 7 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/632?version=7 + name: kmer-profiling-hifi-VGP1/main + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: + - meryl + - genomescope + update_time: '2024-10-13' + versions: 7 +- create_time: '2024-08-07' + creators: + - Debjyoti Ghosh + doi: null + edam_operation: [] + edam_topic: [] + id: '1090' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1090?version=1 + name: qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis + number_of_steps: 3 + source: WorkflowHub + tags: [] + tools: + - Rarefaction + - Taxonomic analysis + - Phylogenetic tree for diversity analysis + update_time: '2024-09-15' + versions: 1 +- create_time: '2024-08-06' + creators: + - Gareth Price + - Anna Syme + doi: null + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence assembly validation + edam_topic: + - Sequence assembly + id: '403' + latest_version: 5 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/403?version=5 + name: Genome-assessment-post-assembly + number_of_steps: 35 + source: WorkflowHub + tags: + - BUSCO + - HiFi + - Merqury + - Meryl + - QC + - Quast + - hifiasm + tools: + - quast + - filter_tabular + - Cut1 + - fastq_to_fasta_python + - merqury + - add_line_to_file + - Add_a_column1 + - fasta-stats + - tp_grep_tool + - tp_sed_tool + - cat1 + - Convert characters1 + - tp_replace_in_column + - Paste1 + - meryl + - datamash_transpose + - busco + update_time: '2024-08-06' + versions: 5 +- create_time: '2024-08-05' + creators: + - Zargham Ahmad + - Helge Hecht + - Wudmir Rojas + doi: 10.48546/workflowhub.workflow.897.2 + edam_operation: [] + edam_topic: [] + id: '897' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/897?version=2 + name: End-to-end EI+ mass spectra prediction workflow using QCxMS + number_of_steps: 14 + source: WorkflowHub + tags: + - Exposomics + - GC-MS + - Metabolomics + - QCxMS + tools: + - qcxms_getres + - split_file_to_collection + - tp_cat + - xtb_molecular_optimization + - qcxms_neutral_run + - 'Remove failed runs + + __FILTER_FAILED_DATASETS__' + - ctb_im_conformers + - tp_cut_tool + - qcxms_production_run + - param_value_from_file + - openbabel_compound_convert + update_time: '2024-10-04' + versions: 2 +- create_time: '2024-08-02' + creators: + - Timon Schlegel + doi: null + edam_operation: [] + edam_topic: [] + id: '1089' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/1089?version=1 + name: Differential peak analysis with SnapATAC2 + number_of_steps: 7 + source: WorkflowHub + tags: [] + tools: + - snapatac2_plotting + - snapatac2_peaks_and_motif + update_time: '2024-08-02' + versions: 1 +- create_time: '2024-07-17' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '1078' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/1078?version=1 + name: Multisample Batch Correction with SnapATAC2 and Harmony + number_of_steps: 29 + source: WorkflowHub + tags: + - scATAC-seq + - single-cell + tools: + - anndata_manipulate + - collection_element_identifiers + - snapatac2_preprocessing + - __EXTRACT_DATASET__ + - snapatac2_plotting + - __FILTER_FROM_FILE__ + - snapatac2_clustering + - Show beginning1 + update_time: '2024-08-02' + versions: 1 +- create_time: '2024-07-17' + creators: + - Timon Schlegel + doi: null + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: '1077' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/1077?version=1 + name: Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 + number_of_steps: 29 + source: WorkflowHub + tags: + - epigenetics + - scATAC-seq + tools: + - anndata_manipulate + - scanpy_filter + - snapatac2_preprocessing + - snapatac2_plotting + - anndata_inspect + - Cut1 + - scanpy_normalize + - scanpy_plot + - replace_column_with_key_value_file + - anndata_ops + - snapatac2_clustering + - scanpy_inspect + update_time: '2024-08-30' + versions: 1 +- create_time: '2024-07-04' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: 10.48546/workflowhub.workflow.1063.2 + edam_operation: + - Variant calling + - Pairwise sequence alignment + edam_topic: [] + id: '1063' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/1063?version=2 + name: allele-based-pathogen-identification/main + number_of_steps: 23 + source: WorkflowHub + tags: [] + tools: + - clair3 + - CONVERTER_gz_to_uncompressed + - table_compute + - snpSift_filter + - Count1 + - Remove beginning1 + - Cut1 + - snpSift_extractFields + - collapse_dataset + - samtools_coverage + - regexColumn1 + - tp_cut_tool + - bcftools_norm + - tp_head_tool + - samtools_depth + - Paste1 + - minimap2 + - bcftools_consensus + update_time: '2024-07-15' + versions: 2 +- create_time: '2024-06-26' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: 10.48546/workflowhub.workflow.1062.1 + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + edam_topic: [] + id: '1062' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1062?version=1 + name: gene-based-pathogen-identification/main + number_of_steps: 15 + source: WorkflowHub + tags: [] + tools: + - abricate + - medaka_consensus_pipeline + - collection_element_identifiers + - split_file_to_collection + - flye + - fasta2tab + - bandage_image + - tab2fasta + - compose_text_param + - tp_find_and_replace + - __BUILD_LIST__ + - param_value_from_file + update_time: '2024-07-15' + versions: 1 +- create_time: '2024-06-26' + creators: + - "B\xE9r\xE9nice Batut" + - Engy Nasr + - Paul Zierep + doi: 10.48546/workflowhub.workflow.1061.1 + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Visualisation + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: '1061' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1061?version=1 + name: nanopore-pre-processing/main + number_of_steps: 25 + source: WorkflowHub + tags: [] + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - krakentools_extract_kraken_reads + - collection_column_join + - Cut1 + - collapse_dataset + - Add_a_column1 + - __FILTER_FAILED_DATASETS__ + - bamtools_split_mapped + - regexColumn1 + - kraken2 + - porechop + - Grep1 + - minimap2 + - multiqc + update_time: '2024-07-15' + versions: 1 +- create_time: '2024-06-26' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: 10.48546/workflowhub.workflow.1060.1 + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Visualisation + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Mapping + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: '1060' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1060?version=1 + name: pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main + number_of_steps: 60 + source: WorkflowHub + tags: [] + tools: + - collection_column_join + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - ggplot2_heatmap + - fasta2tab + - tp_replace_in_column + - tp_sorted_uniq + - clustalw + - Remove beginning1 + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - tp_split_on_column + - newick_display + - Count1 + - regexColumn1 + - bedtools_getfastabed + - tp_multijoin_tool + - Cut1 + - fasttree + - tab2fasta + - __FILTER_EMPTY_DATASETS__ + - regex1 + update_time: '2024-07-15' + versions: 1 +- create_time: '2024-06-26' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: 10.48546/workflowhub.workflow.1059.1 + edam_operation: + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: '1059' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/1059?version=1 + name: taxonomy-profiling-and-visualization-with-krona/main + number_of_steps: 3 + source: WorkflowHub + tags: [] + tools: + - kraken2 + - krakentools_kreport2krona + - taxonomy_krona_chart + update_time: '2024-07-15' + versions: 1 +- create_time: '2024-06-28' + creators: + - Delphine Lariviere + doi: null + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: '1057' + latest_version: 2 + license: null + link: https://workflowhub.eu/workflows/1057?version=2 + name: Plot-Nx-Size/main + number_of_steps: 14 + source: WorkflowHub + tags: [] + tools: + - sort1 + - addName + - collapse_dataset + - Add_a_column1 + - Cut1 + - datamash_ops + - gfastats + - param_value_from_file + - tp_awk_tool + - compose_text_param + - ggplot2_point + - addValue + update_time: '2024-06-28' + versions: 2 +- create_time: '2024-06-21' + creators: + - VGP Project + doi: 10.48546/workflowhub.workflow.1054.1 + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: '1054' + latest_version: 1 + license: GPL-3.0+ + link: https://workflowhub.eu/workflows/1054?version=1 + name: TSI-Scaffolding-with-HiC (based on VGP-HiC-scaffolding) + number_of_steps: 25 + source: WorkflowHub + tags: + - TSI + tools: + - bwa_mem2 + - '' + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - busco + update_time: '2024-06-21' + versions: 1 +- create_time: '2024-06-20' + creators: + - Luke Silver + - Anna Syme + doi: 10.48546/workflowhub.workflow.875.3 + edam_operation: + - Genome annotation + - Repeat sequence detection + edam_topic: [] + id: '875' + latest_version: 3 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/875?version=3 + name: Repeat masking - TSI + number_of_steps: 2 + source: WorkflowHub + tags: + - TSI-annotation + tools: + - repeatmasker_wrapper + - repeatmodeler + update_time: '2024-06-20' + versions: 3 +- create_time: '2024-10-10' + creators: + - Lucille Delisle + doi: null + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Genome annotation + edam_topic: [] + id: '1051' + latest_version: 2 + license: GPL-3.0-or-later + link: https://workflowhub.eu/workflows/1051?version=2 + name: brew3r/main + number_of_steps: 5 + source: WorkflowHub + tags: [] + tools: + - stringtie + - map_param_value + - stringtie_merge + - brew3r_r + update_time: '2024-10-10' + versions: 2 +- create_time: '2024-10-12' + creators: + - ABRomics None + - Pierre Marin + - Clea Siguret + doi: null + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: '1050' + latest_version: 8 + license: GPL-3.0-or-later + link: https://workflowhub.eu/workflows/1050?version=8 + name: bacterial_genome_annotation/main + number_of_steps: 6 + source: WorkflowHub + tags: + - ABRomics + - Annotation + - Genomics + - bacterial-genomics + - fasta + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-10-12' + versions: 8 +- create_time: '2024-10-12' + creators: + - ABRomics None + - Pierre Marin + - Clea Siguret + doi: null + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: '1049' + latest_version: 6 + license: GPL-3.0-or-later + link: https://workflowhub.eu/workflows/1049?version=6 + name: amr_gene_detection/main + number_of_steps: 5 + source: WorkflowHub + tags: + - ABRomics + - AMR + - AMR-detection + - Genomics + - antibiotic-resistance + - antimicrobial resistance + - antimicrobial-resistance-genes + - bacterial-genomics + - fasta + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-10-12' + versions: 6 +- create_time: '2024-06-18' + creators: + - Luke Silver + doi: 10.48546/workflowhub.workflow.881.4 + edam_operation: + - Scaffolding + - Transcriptome assembly + - Sequence assembly validation + - Genome assembly + edam_topic: [] + id: '881' + latest_version: 4 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/881?version=4 + name: Fgenesh annotation -TSI + number_of_steps: 9 + source: WorkflowHub + tags: + - TSI-annotation + tools: + - fgenesh_get_proteins + - fgenesh_get_mrnas_gc + - fgenesh_merge + - fgenesh_annotate + - fgenesh_split + - busco + update_time: '2024-06-18' + versions: 4 +- create_time: '2024-06-07' + creators: + - Peter van Heusden + doi: null + edam_operation: + - Sequence alignment analysis + - Taxonomic classification + - Phylogenetic tree generation + - Local alignment + - Global alignment + - Phylogenetic tree visualisation + - Sequence contamination filtering + - Variant calling + - Sequence analysis + - Validation + - Antimicrobial resistance prediction + - Sequence alignment + - Sequencing quality control + edam_topic: + - Genetic variation + - Infectious disease + - Microbiology + - Public health and epidemiology + - Sequence assembly + id: '1035' + latest_version: 1 + license: AGPL-3.0-or-later + link: https://workflowhub.eu/workflows/1035?version=1 + name: TB Variant Analysis v1.0 + number_of_steps: 15 + source: WorkflowHub + tags: + - pathogen + - tuberculosis + tools: + - fastp + - snippy + - 'EMBOSS: seqret84' + - mosdepth + - tbvcfreport + - tp_sed_tool + - kraken2 + - qualimap_bamqc + - tp_awk_tool + - __FLATTEN__ + - tb_variant_filter + - multiqc + - tb_profiler_profile + - bcftools_consensus + update_time: '2024-06-12' + versions: 1 +- create_time: '2024-06-06' + creators: + - Zargham Ahmad + - Helge Hecht + - Elliott J. Price + doi: 10.48546/workflowhub.workflow.888.2 + edam_operation: + - Spectral library search + - Format validation + - Filtering + - Annotation + - Standardisation and normalisation + edam_topic: + - Compound libraries and screening + - Computational chemistry + - Data mining + - Small molecules + id: '888' + latest_version: 2 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/888?version=2 + name: Theoretical fragment substructure generation and in silico mass spectral library + high-resolution upcycling workflow + number_of_steps: 22 + source: WorkflowHub + tags: + - Bioinformatics + - Cheminformatics + - Metabolomics + tools: + - recetox_msfinder + - matchms_metadata_export + - rem_complex + - column_remove_by_header + - csv_to_tabular + - matchms_remove_key + - tabular_to_csv + - matchms_convert + - matchms_filtering + - tp_find_and_replace + - matchms_add_key + - msmetaenhancer + - matchms_subsetting + - use_theoretical_mz_annotations + update_time: '2024-06-19' + versions: 2 +- create_time: '2024-05-30' + creators: + - Debjyoti Ghosh + doi: null + edam_operation: [] + edam_topic: [] + id: '893' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/893?version=1 + name: qiime2-I-import/Ia-import-multiplexed-se + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: + - qiime2__demux__emp_single + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-07-13' + versions: 1 +- create_time: '2024-05-30' + creators: + - Debjyoti Ghosh + doi: null + edam_operation: [] + edam_topic: [] + id: '892' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/892?version=1 + name: qiime2-II-denoising/IIa-denoising-se + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: + - qiime2__feature_table__summarize + - qiime2__dada2__denoise_single + - qiime2__feature_table__tabulate_seqs + - qiime2__metadata__tabulate + update_time: '2024-07-13' + versions: 1 +- create_time: '2023-11-09' + creators: + - Sarah Williams + - Mike Thang + - Valentine Murigneaux + doi: null + edam_operation: [] + edam_topic: [] + id: '647' + latest_version: 1 + license: other-closed + link: https://workflowhub.eu/workflows/647?version=1 + name: scRNAseq Single Sample Processing Cell Ranger + number_of_steps: 3 + source: WorkflowHub + tags: + - scRNAseq + tools: + - '' + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Sarah Williams + - Mike Thang + - Valentine Murigneaux + doi: null + edam_operation: [] + edam_topic: + - Gene expression + - Transcriptomics + id: '646' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/646?version=2 + name: 'scRNAseq: Count and Load with Cell Ranger' + number_of_steps: 6 + source: WorkflowHub + tags: + - scRNAseq + tools: + - anndata_manipulate + - tp_text_file_with_recurring_lines + - anndata_inspect + - scanpy_read_10x + - tp_sed_tool + - cellranger + update_time: '2024-05-30' + versions: 2 +- create_time: '2024-05-30' + creators: + - Sarah Williams + - Mike Thang + - Valentine Murigneaux + doi: null + edam_operation: [] + edam_topic: + - Gene expression + - Transcriptomics + id: '514' + latest_version: 3 + license: MIT + link: https://workflowhub.eu/workflows/514?version=3 + name: scRNAseq Single Sample Processing Counts Matrix + number_of_steps: 3 + source: WorkflowHub + tags: + - scRNAseq + tools: + - '' + update_time: '2024-05-30' + versions: 3 +- create_time: '2023-12-12' + creators: + - Sarah Williams + - Mike Thang + - Valentine Murigneaux + doi: null + edam_operation: [] + edam_topic: [] + id: '465' + latest_version: 4 + license: MIT + link: https://workflowhub.eu/workflows/465?version=4 + name: scRNAseq Single Sample Processing STARSolo + number_of_steps: 3 + source: WorkflowHub + tags: + - scRNAseq + tools: + - '' + update_time: '2024-05-30' + versions: 4 +- create_time: '2024-05-30' + creators: + - Sarah Williams + - Mike Thang + - Valentine Murigneaux + doi: null + edam_operation: + - Differential gene expression analysis + edam_topic: + - Gene expression + - Transcriptomics + id: '468' + latest_version: 3 + license: MIT + link: https://workflowhub.eu/workflows/468?version=3 + name: scRNAseq_QCtoBasicProcessing + number_of_steps: 15 + source: WorkflowHub + tags: + - scRNAseq + tools: + - scanpy_find_cluster + - scanpy_scale_data + - scanpy_plot_embed + - scanpy_compute_graph + - scanpy_find_markers + - anndata_inspect + - scanpy_normalise_data + - scanpy_run_umap + - tp_head_tool + - scanpy_plot + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2024-05-30' + versions: 3 +- create_time: '2024-05-30' + creators: + - Sarah Williams + - Mike Thang + - Valentine Murigneaux + doi: null + edam_operation: + - Differential gene expression analysis + edam_topic: + - Gene expression + - Transcriptomics + id: '467' + latest_version: 4 + license: MIT + link: https://workflowhub.eu/workflows/467?version=4 + name: scRNAseq_CellQC + number_of_steps: 6 + source: WorkflowHub + tags: + - scRNAseq + tools: + - scanpy_filter_cells + - scanpy_plot + - scanpy_multiplet_scrublet + - anndata_ops + update_time: '2024-05-30' + versions: 4 +- create_time: '2024-05-30' + creators: + - Sarah Williams + - Mike Thang + - Valentine Murigneaux + doi: null + edam_operation: + - Sequence alignment + edam_topic: + - Gene expression + - Transcriptomics + id: '513' + latest_version: 3 + license: MIT + link: https://workflowhub.eu/workflows/513?version=3 + name: 'scRNAseq: Count and Load with starSOLO' + number_of_steps: 9 + source: WorkflowHub + tags: + - scRNAseq + tools: + - anndata_manipulate + - tp_text_file_with_recurring_lines + - rna_starsolo + - __UNZIP_COLLECTION__ + - anndata_inspect + - scanpy_read_10x + - collapse_dataset + - tp_sed_tool + update_time: '2024-05-30' + versions: 3 +- create_time: '2024-05-30' + creators: + - Sarah Williams + - Mike Thang + - Valentine Murigneaux + doi: null + edam_operation: [] + edam_topic: + - Gene expression + - Transcriptomics + id: '512' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/512?version=2 + name: 'scRNAseq: Load counts matrix' + number_of_steps: 5 + source: WorkflowHub + tags: + - scRNAseq + tools: + - anndata_manipulate + - tp_text_file_with_recurring_lines + - anndata_inspect + - scanpy_read_10x + - tp_sed_tool + update_time: '2024-05-30' + versions: 2 +- create_time: '2024-05-08' + creators: + - Luke Silver + - Anna Syme + doi: 10.48546/workflowhub.workflow.880.1 + edam_operation: + - Sequence file editing + - Data handling + edam_topic: [] + id: '880' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/880?version=1 + name: Convert formats - TSI + number_of_steps: 47 + source: WorkflowHub + tags: + - TSI-annotation + tools: + - Cut1 + - tp_sort_header_tool + - seqtk_seq + - tp_replace_in_line + - fasta2tab + - tp_grep_tool + - tp_sed_tool + - tp_awk_tool + - tab2fasta + - Paste1 + - seqtk_subseq + - fasta_compute_length + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-08' + creators: + - Luke Silver + - Anna Syme + doi: 10.48546/workflowhub.workflow.879.1 + edam_operation: + - Scaffolding + - Transcriptome assembly + - de Novo sequencing + - Genome assembly + - De-novo assembly + - Sequence assembly validation + - Coding region prediction + edam_topic: [] + id: '879' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/879?version=1 + name: Extract transcripts - TSI + number_of_steps: 3 + source: WorkflowHub + tags: + - TSI-annotation + tools: + - tp_sed_tool + - transdecoder + - busco + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-08' + creators: + - Luke Silver + - Anna Syme + doi: 10.48546/workflowhub.workflow.878.1 + edam_operation: + - Mapping + - Transcriptome assembly + - RNA-Seq analysis + edam_topic: [] + id: '878' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/878?version=1 + name: Combine transcripts - TSI + number_of_steps: 8 + source: WorkflowHub + tags: + - TSI-annotation + tools: + - 'skipping 1 header line + + Filter1' + - gtftobed12 + - seq_filter_by_id + - cpat + - tp_cut_tool + - tp_sed_tool + - bedtools_getfastabed + - stringtie_merge + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-08' + creators: + - Luke Silver + - Anna Syme + doi: 10.48546/workflowhub.workflow.877.1 + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Sequence alignment + edam_topic: [] + id: '877' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/877?version=1 + name: Find transcripts - TSI + number_of_steps: 2 + source: WorkflowHub + tags: + - TSI-annotation + tools: + - stringtie + - hisat2 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-08' + creators: + - Luke Silver + - Anna Syme + doi: 10.48546/workflowhub.workflow.876.1 + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: '876' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/876?version=1 + name: QC and trimming of RNAseq reads - TSI + number_of_steps: 14 + source: WorkflowHub + tags: + - TSI-annotation + tools: + - fastqc + - trimmomatic + - Remove beginning1 + - __EXTRACT_DATASET__ + - Cut1 + - tp_cat + - tp_replace_in_column + - multiqc + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-04-23' + creators: + - Andrii Neronov + - "Th\xE9o Boyer" + doi: 10.48546/workflowhub.workflow.831.1 + edam_operation: [] + edam_topic: [] + id: '831' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/831?version=1 + name: SGWB model spectrum + number_of_steps: 1 + source: WorkflowHub + tags: + - astronomy + tools: + - sgwb_astro_tool + update_time: '2024-04-23' + versions: 1 +- create_time: '2024-04-18' + creators: + - Andrii Neronov + - "Th\xE9o Boyer" + - Denys Savchenko + - Volodymyr Savchenko + doi: 10.48546/workflowhub.workflow.815.2 + edam_operation: [] + edam_topic: + - Physics + id: '815' + latest_version: 2 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/815?version=2 + name: Stochastic Gravitational Wave Backgorund (SGWB) tool + number_of_steps: 2 + source: WorkflowHub + tags: + - astronomy + tools: + - sgwb_astro_tool + update_time: '2024-04-18' + versions: 2 +- create_time: '2024-03-28' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '807' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/807?version=1 + name: A workflow demonstrating the 'Run interpolation based on IDW' tool + number_of_steps: 5 + source: WorkflowHub + tags: [] + tools: + - tabular_to_csv + - graphicsmagick_image_compare + - interpolation_run_idw_interpolation + - Filter1 + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-08-06' + creators: + - Gareth Price + - Anna Syme + doi: null + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: '794' + latest_version: 2 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/794?version=2 + name: Genome-assessment-post-assembly + number_of_steps: 35 + source: WorkflowHub + tags: + - BUSCO + - HiFi + - Merqury + - Meryl + - QC + - Quast + - hifiasm + tools: + - quast + - filter_tabular + - Cut1 + - fastq_to_fasta_python + - merqury + - add_line_to_file + - Add_a_column1 + - fasta-stats + - tp_grep_tool + - tp_sed_tool + - cat1 + - Convert characters1 + - tp_replace_in_column + - Paste1 + - meryl + - datamash_transpose + - busco + update_time: '2024-08-06' + versions: 2 +- create_time: '2024-05-30' + creators: + - Matthias Bernt + doi: null + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: '790' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/790?version=2 + name: dada2/main + number_of_steps: 14 + source: WorkflowHub + tags: + - name:amplicon + tools: + - dada2_makeSequenceTable + - __UNZIP_COLLECTION__ + - dada2_seqCounts + - dada2_assignTaxonomyAddspecies + - dada2_filterAndTrim + - __APPLY_RULES__ + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2024-06-02' + versions: 2 +- create_time: '2024-03-11' + creators: + - Diego De Panis + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Optimisation and refinement + - Scaffolding + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly visualisation + - Sequence alignment + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '789' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/789?version=1 + name: ERGA ONT+Illumina Assembly+QC NextDenovo+HyPo v2403 (WF2) + number_of_steps: 21 + source: WorkflowHub + tags: + - name:ASSEMBLY+QC + - name:ERGA + - name:ILLUMINA + - name:ONT + tools: + - bwa_mem2 + - sam_merge2 + - Add_a_column1 + - merqury + - datamash_ops + - nextdenovo + - gfastats + - __FLATTEN__ + - gfa_to_fa + - hypo + - minimap2 + - bandage_image + - param_value_from_file + - busco + - tables_arithmetic_operations + update_time: '2024-03-11' + versions: 1 +- create_time: '2024-03-11' + creators: + - Diego De Panis + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Optimisation and refinement + - Scaffolding + - Pairwise sequence alignment + - Transcriptome assembly + - Cross-assembly + - Mapping assembly + - Sequence assembly visualisation + - Sequence alignment + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '788' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/788?version=1 + name: ERGA ONT+Illumina Assembly+QC Flye+HyPo v2403 (WF2) + number_of_steps: 16 + source: WorkflowHub + tags: + - name:ASSEMBLY+QC + - name:ERGA + - name:ILLUMINA + - name:ONT + tools: + - bwa_mem2 + - sam_merge2 + - flye + - merqury + - gfastats + - __FLATTEN__ + - hypo + - minimap2 + - bandage_image + - param_value_from_file + - busco + update_time: '2024-03-11' + versions: 1 +- create_time: '2024-03-06' + creators: + - Christian Tischer + doi: null + edam_operation: [] + edam_topic: [] + id: '782' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/782?version=1 + name: Wound Healing Scrath Assay Image Analysis + number_of_steps: 1 + source: WorkflowHub + tags: + - Bioimage + - imageJ + tools: + - woundhealing_scratch_assay + update_time: '2024-03-06' + versions: 1 +- create_time: '2024-03-05' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.778.1 + edam_operation: [] + edam_topic: [] + id: '778' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/778?version=1 + name: Galaxy Molecular Structure Checking + number_of_steps: 19 + source: WorkflowHub + tags: [] + tools: + - biobb_amber_amber_to_pdb_ext + - biobb_amber_leap_gen_top_ext + - biobb_amber_sander_mdrun_ext + - biobb_io_pdb_ext + - biobb_model_fix_altlocs_ext + - biobb_structure_utils_extract_model_ext + - biobb_model_fix_amides_ext + - biobb_structure_utils_remove_pdb_water_ext + - biobb_structure_utils_extract_chain_ext + - biobb_structure_utils_remove_molecules_ext + - biobb_model_fix_chirality_ext + - biobb_chemistry_reduce_remove_hydrogens_ext + - biobb_model_fix_side_chain_ext + - biobb_io_canonical_fasta_ext + - biobb_model_fix_ssbonds_ext + - biobb_structure_utils_structure_check_ext + - biobb_model_fix_backbone_ext + update_time: '2024-03-05' + versions: 1 +- create_time: '2024-03-01' + creators: + - Leonid Kostrykin + doi: null + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: '771' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/771?version=1 + name: fluorescence-nuclei-segmentation-and-counting/main + number_of_steps: 7 + source: WorkflowHub + tags: [] + tools: + - ip_convertimage + - ip_threshold + - ip_overlay_images + - ip_count_objects + - ip_binary_to_labelimage + - ip_filter_standard + - ip_histogram_equalization + update_time: '2024-03-06' + versions: 1 +- create_time: '2024-02-16' + creators: + - Bryan Raubenolt + doi: 10.48546/workflowhub.workflow.762.1 + edam_operation: [] + edam_topic: [] + id: '762' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/762?version=1 + name: flavivirushelicase_apo + number_of_steps: 25 + source: WorkflowHub + tags: + - dengue + - helicase + - molecular dynamics + - rna virus + - west nile + - zika + tools: + - gmx_rmsf + - gmx_get_builtin_file + - gmx_rmsd + - __EXTRACT_DATASET__ + - acpype_Amber2Gromacs + - gmx_sim + - gmx_em + - gmx_solvate + - tp_grep_tool + - gmx_restraints + - gromacs_modify_topology + - tleap + - gmx_makendx + - gmx_trj + - gmx_editconf + update_time: '2024-03-02' + versions: 1 +- create_time: '2024-02-16' + creators: + - Bryan Raubenolt + doi: 10.48546/workflowhub.workflow.763.1 + edam_operation: [] + edam_topic: [] + id: '763' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/763?version=1 + name: coronavirushelicase_proteindrugcomplex + number_of_steps: 25 + source: WorkflowHub + tags: + - MERS + - NSP13 + - SARS-CoV-2 + - coronavirus + - covid-19 + - covid19.galaxyproject.org + - helicase + - molecular dynamics + - rna virus + tools: + - gmx_rmsf + - gmx_get_builtin_file + - gmx_rmsd + - __EXTRACT_DATASET__ + - acpype_Amber2Gromacs + - gmx_sim + - gmx_em + - gmx_solvate + - tp_grep_tool + - gmx_restraints + - gromacs_modify_topology + - tleap + - gmx_makendx + - gmx_trj + - gmx_editconf + update_time: '2024-03-02' + versions: 1 +- create_time: '2024-02-16' + creators: + - Bryan Raubenolt + doi: 10.48546/workflowhub.workflow.764.1 + edam_operation: [] + edam_topic: [] + id: '764' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/764?version=1 + name: coronavirushelicase_apo + number_of_steps: 25 + source: WorkflowHub + tags: + - MERS + - NSP13 + - SARS-CoV-2 + - coronavirus + - covid-19 + - covid19.galaxyproject.org + - helicase + - molecular dynamics + - rna virus + tools: + - gmx_rmsf + - gmx_get_builtin_file + - gmx_rmsd + - __EXTRACT_DATASET__ + - acpype_Amber2Gromacs + - gmx_sim + - gmx_em + - gmx_solvate + - tp_grep_tool + - gmx_restraints + - gromacs_modify_topology + - tleap + - gmx_makendx + - gmx_trj + - gmx_editconf + update_time: '2024-03-02' + versions: 1 +- create_time: '2024-02-16' + creators: + - Bryan Raubenolt + doi: 10.48546/workflowhub.workflow.761.1 + edam_operation: [] + edam_topic: [] + id: '761' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/761?version=1 + name: flavivirushelicase_proteindrugcomplex + number_of_steps: 25 + source: WorkflowHub + tags: + - NS3 + - dengue + - helicase + - molecular dynamics + - rna virus + - west nile + - zika + tools: + - gmx_rmsf + - gmx_get_builtin_file + - gmx_rmsd + - __EXTRACT_DATASET__ + - acpype_Amber2Gromacs + - gmx_sim + - gmx_em + - gmx_solvate + - tp_grep_tool + - gmx_restraints + - gromacs_modify_topology + - tleap + - gmx_makendx + - gmx_trj + - gmx_editconf + update_time: '2024-03-02' + versions: 1 +- create_time: '2024-02-21' + creators: + - Volodymyr Savchenko + - Denys Savchenko + - Andrii Neronov + doi: null + edam_operation: [] + edam_topic: [] + id: '766' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/766?version=1 + name: Example Multi-Wavelength Light-Curve Analysis + number_of_steps: 5 + source: WorkflowHub + tags: + - astronomy + tools: + - lightcurve_analysis_astro_tool_pr91 + - grb-detection_astro_tool + - hess_astro_tool + update_time: '2024-03-01' + versions: 1 +- create_time: '2024-02-14' + creators: + - Anthony Bretaudeau + doi: null + edam_operation: + - Genome visualisation + edam_topic: [] + id: '749' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/749?version=1 + name: Refining Genome Annotations with Apollo (prokaryotes) + number_of_steps: 5 + source: WorkflowHub + tags: + - genome-annotation + tools: + - list_organism + - create_account + - jbrowse + - iframe + - create_or_update + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - "Marie Joss\xE9" + doi: null + edam_operation: [] + edam_topic: [] + id: '759' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/759?version=1 + name: Visualizing NDVI time-series data with HoloViz + number_of_steps: 2 + source: WorkflowHub + tags: + - Ecology + tools: + - interactive_tool_holoviz + - interactive_tool_copernicus_notebook + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - Marie Josse + doi: null + edam_operation: [] + edam_topic: [] + id: '758' + latest_version: 1 + license: CC-BY-SA-4.0 + link: https://workflowhub.eu/workflows/758?version=1 + name: Calculating and visualizing OBIS marine biodiversity indicators + number_of_steps: 3 + source: WorkflowHub + tags: + - Ecology + tools: + - tp_cut_tool + - csv_to_tabular + - obisindicators + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - Leandro Liborio + doi: null + edam_operation: [] + edam_topic: [] + id: '757' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/757?version=1 + name: Finding the Muon Stopping Site using PyMuonSuite + number_of_steps: 2 + source: WorkflowHub + tags: [] + tools: + - pm_muairss_read + - pm_uep_opt + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - "Marie Joss\xE9" + doi: null + edam_operation: [] + edam_topic: [] + id: '756' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/756?version=1 + name: Sentinel 5P volcanic data visualization + number_of_steps: 2 + source: WorkflowHub + tags: + - Climate + tools: + - interactive_tool_panoply + - interactive_tool_copernicus_notebook + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - Anthony Bretaudeau + doi: null + edam_operation: + - Fold recognition + - Genome annotation + - Protein feature detection + - Information extraction + - Query and retrieval + - Sequence motif recognition + - Homology-based gene prediction + edam_topic: [] + id: '755' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/755?version=1 + name: Functional protein annotation using EggNOG-mapper and InterProScan + number_of_steps: 2 + source: WorkflowHub + tags: + - genome-annotation + tools: + - eggnog_mapper + - interproscan + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - Anthony Bretaudeau + doi: null + edam_operation: + - Fold recognition + - Genome visualisation + - Protein feature detection + - Information extraction + - Genome assembly + - Query and retrieval + - Sequence motif recognition + - Sequence annotation + - Homology-based gene prediction + - Scaffolding + - Genome annotation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: '754' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/754?version=1 + name: Genome annotation with Funannotate + number_of_steps: 9 + source: WorkflowHub + tags: + - genome-annotation + tools: + - aegean_parseval + - funannotate_predict + - eggnog_mapper + - jbrowse + - interproscan + - rna_star + - funannotate_compare + - busco + - funannotate_annotate + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - Anthony Bretaudeau + doi: null + edam_operation: + - Genome annotation + - Editing + - RNA-Seq analysis + edam_topic: [] + id: '753' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/753?version=1 + name: Masking repeats with RepeatMasker + number_of_steps: 2 + source: WorkflowHub + tags: + - genome-annotation + tools: + - repeatmasker_wrapper + - red + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-03-27' + creators: + - Anna Syme + doi: null + edam_operation: + - Visualisation + - Cross-assembly + - Mapping assembly + - Genome assembly + - De-novo assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: '750' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/750?version=2 + name: assembly-with-flye/main + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: + - fasta-stats + - bandage_image + - quast + - flye + update_time: '2024-06-13' + versions: 2 +- create_time: '2024-02-08' + creators: + - VGP + - ' Galaxy' + doi: null + edam_operation: [] + edam_topic: [] + id: '738' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/738?version=1 + name: Mitogenome-assembly-VGP0/main + number_of_steps: 3 + source: WorkflowHub + tags: + - Reviewed + - vgp + tools: + - mitohifi + - compress_file + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-03-14' + creators: + - Lucille Delisle + doi: null + edam_operation: [] + edam_topic: [] + id: '715' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/715?version=2 + name: velocyto/Velocyto-on10X-from-bundled + number_of_steps: 2 + source: WorkflowHub + tags: + - name:single-cell + tools: + - '' + - __APPLY_RULES__ + update_time: '2024-04-20' + versions: 2 +- create_time: '2024-01-09' + creators: + - Diego De Panis + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '702' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/702?version=1 + name: ERGA HiC Collapsed Scaffolding+QC YaHS v2311 (WF4) + number_of_steps: 16 + source: WorkflowHub + tags: + - ERGA + - HiC + - name:ASSEMBLY+QC + tools: + - bwa_mem2 + - yahs + - merqury + - pretext_snapshot + - gfastats + - pretext_map + - gfa_to_fa + - bellerophon + - param_value_from_file + - busco + update_time: '2024-01-09' + versions: 1 +- create_time: '2024-01-09' + creators: + - Diego De Panis + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '701' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/701?version=1 + name: ERGA ONT+Illumina Collapsed Purge+QC v2311 (WF3) + number_of_steps: 14 + source: WorkflowHub + tags: + - ERGA + - illumina + - name:ASSEMBLY+QC + tools: + - merqury + - gfastats + - gfa_to_fa + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-01-09' + versions: 1 +- create_time: '2024-01-08' + creators: + - Diego De Panis + doi: null + edam_operation: + - Sequence trimming + - k-mer counting + - Genotyping + edam_topic: + - Whole genome sequencing + id: '698' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/698?version=1 + name: ERGA Profiling Illumina v2311 (WF1) + number_of_steps: 17 + source: WorkflowHub + tags: + - ERGA + - illumina + - name:PROFILING + tools: + - Cut1 + - genomescope + - Add_a_column1 + - tp_grep_tool + - tp_cut_tool + - smudgeplot + - Convert characters1 + - tp_find_and_replace + - meryl + - param_value_from_file + update_time: '2024-01-08' + versions: 1 +- create_time: '2024-01-08' + creators: + - Diego De Panis + doi: null + edam_operation: + - Sequence trimming + - Sequence conversion + - DNA transcription + - Box-Whisker plot plotting + - DNA translation + - Scatter plot plotting + edam_topic: + - Whole genome sequencing + id: '697' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/697?version=1 + name: ERGA DataQC ONT v2311 (WF0) + number_of_steps: 3 + source: WorkflowHub + tags: + - DataQC + - ERGA + - ONT + tools: + - seqkit_stats + - nanoplot + - collapse_dataset + update_time: '2024-01-08' + versions: 1 +- create_time: '2024-01-02' + creators: + - Diego De Panis + doi: 10.48546/workflowhub.workflow.606.2 + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '606' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/606?version=2 + name: ERGA HiFi Hap1Hap2 Purge+QC v2309 (WF3) + number_of_steps: 24 + source: WorkflowHub + tags: + - Assembly+QC + - ERGA + - HiFi + tools: + - merqury + - gfastats + - gfa_to_fa + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-03-13' + versions: 1 +- create_time: '2024-10-07' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: null + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: '694' + latest_version: 5 + license: MIT + link: https://workflowhub.eu/workflows/694?version=5 + name: fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex + number_of_steps: 6 + source: WorkflowHub + tags: + - '#single-cell' + tools: + - '' + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-10-07' + versions: 5 +- create_time: '2023-12-19' + creators: + - Iacopo Cristoferi + - Helena Rasche + doi: null + edam_operation: + - RNA-Seq analysis + - Annotation + - Gene functional annotation + edam_topic: [] + id: '689' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/689?version=1 + name: 'mRNA-Seq BY-COVID Pipeline: Analysis' + number_of_steps: 15 + source: WorkflowHub + tags: + - BY-COVID + - covid-19 + tools: + - collection_column_join + - annotatemyids + - __EXTRACT_DATASET__ + - tp_sort_header_tool + - tp_replace_in_line + - Cut1 + - Add_a_column1 + - join1 + - goseq + - tp_sorted_uniq + - limma_voom + update_time: '2024-01-24' + versions: 1 +- create_time: '2023-12-19' + creators: + - Iacopo Cristoferi + - Helena Rasche + doi: null + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: '688' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/688?version=1 + name: 'mRNA-Seq BY-COVID Pipeline: Counts' + number_of_steps: 8 + source: WorkflowHub + tags: + - BY-COVID + - covid-19 + tools: + - fastqc + - rseqc_read_distribution + - rseqc_geneBody_coverage + - cutadapt + - multiqc + - featurecounts + - hisat2 + update_time: '2024-01-24' + versions: 1 +- create_time: '2023-12-06' + creators: + - Iacopo Cristoferi + - Helena Rasche + doi: null + edam_operation: [] + edam_topic: [] + id: '685' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/685?version=1 + name: mRNA-Seq BY-COVID Pipeline + number_of_steps: 18 + source: WorkflowHub + tags: + - BY-COVID + - covid-19 + tools: [] + update_time: '2023-12-06' + versions: 1 +- create_time: '2023-11-25' + creators: + - workflow4metabolomics + doi: null + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: '680' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/680?version=1 + name: gcms-metams/main + number_of_steps: 7 + source: WorkflowHub + tags: + - GC-MS + - GTN + - MS + - Metabolomics + - metaMS + - workflow4metabolomics + tools: + - xcms_merge + - checkFormat + - Multivariate + - metams_runGC + - abims_xcms_xcmsSet + - msnbase_readmsdata + - xcms_plot_chromatogram + update_time: '2024-06-13' + versions: 1 +- create_time: '2023-11-28' + creators: + - Simon Bray + doi: null + edam_operation: [] + edam_topic: [] + id: '248' + latest_version: 4 + license: MIT + link: https://workflowhub.eu/workflows/248?version=4 + name: gromacs-mmgbsa/main + number_of_steps: 18 + source: WorkflowHub + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - d354bc62a13564f8 + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2024-07-01' + versions: 4 +- create_time: '2023-11-24' + creators: + - workflow4metabolomics + doi: null + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: '677' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/677?version=1 + name: lcms-preprocessing/main + number_of_steps: 11 + source: WorkflowHub + tags: + - GTN + - LC-MS + - MS + - Metabolomics + - workflow4metabolomics + - xcms + tools: + - xcms_merge + - intens_check + - abims_xcms_fillPeaks + - abims_xcms_retcor + - abims_xcms_group + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - xcms_plot_chromatogram + update_time: '2024-07-13' + versions: 1 +- create_time: '2023-11-23' + creators: + - khaled Jumah + - Katarzyna Kamieniecka + - Wolfgang Maier + - Krzysztof Poterlowicz + doi: 10.48546/workflowhub.workflow.676.1 + edam_operation: + - Statistical calculation + - Genome alignment + - Sequence composition calculation + - Genome indexing + - Read mapping + - Variant calling + - Validation + - Copy number estimation + - Generation + - Sequencing quality control + - Sequence alignment + - Sequence visualisation + edam_topic: + - Copy number variation + - Data visualisation + - Genetic variation + id: '676' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/676?version=1 + name: Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC + number_of_steps: 30 + source: WorkflowHub + tags: + - MIRACUM + - hCNV + - variant-analysis + tools: + - fastqc + - control_freec + - tp_text_file_with_recurring_lines + - trimmomatic + - samtools_calmd + - samtools_view + - __EXTRACT_DATASET__ + - tp_replace_in_line + - samtools_rmdup + - __RELABEL_FROM_FILE__ + - Grep1 + - bamleftalign + - multiqc + - __BUILD_LIST__ + - circos + - bwa_mem + update_time: '2024-04-03' + versions: 1 +- create_time: '2023-10-26' + creators: + - Valentine Murigneux + - Mike Thang + - Saskia Hiltemann + - "B\xE9r\xE9nice Batut" + doi: 10.48546/workflowhub.workflow.624.1 + edam_operation: + - Phylogenetic tree analysis + - Visualisation + - Nucleic acid sequence analysis + edam_topic: + - Metagenomic sequencing + - Metagenomics + id: '624' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/624?version=1 + name: Analyses of shotgun metagenomics data with MetaPhlAn2 + number_of_steps: 17 + source: WorkflowHub + tags: + - GUCFG2galaxy + - Metagenomics + - shotgun + tools: + - '' + - metaphlan2krona + - merge_metaphlan_tables + - taxonomy_krona_chart + - Cut1 + - humann2_renorm_table + - metaphlan2 + - humann2 + - humann2_regroup_table + update_time: '2024-04-05' + versions: 1 +- create_time: '2023-11-10' + creators: + - "Marie Joss\xE9" + - Yvan Le Bras + doi: null + edam_operation: [] + edam_topic: + - Biodiversity + - Ecology + id: '662' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/662?version=1 + name: Obis biodiversity indicator on Asian pacific + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: + - tp_cut_tool + - csv_to_tabular + - obisindicators + - Filter1 + update_time: '2023-11-10' + versions: 1 +- create_time: '2023-11-10' + creators: + - "Marie Joss\xE9" + - Yvan Le Bras + doi: null + edam_operation: [] + edam_topic: + - Biodiversity + - Ecology + id: '661' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/661?version=1 + name: Boulder fields indicators + number_of_steps: 3 + source: WorkflowHub + tags: [] + tools: + - cb_ivr + - cb_div + - cb_dissim + update_time: '2023-11-10' + versions: 1 +- create_time: '2023-11-10' + creators: + - Yvan Le Bras + doi: null + edam_operation: [] + edam_topic: + - Biodiversity + - Ecology + id: '660' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/660?version=1 + name: SPIPOLL MMOS GAPARS crowdsourcing results + number_of_steps: 12 + source: WorkflowHub + tags: [] + tools: + - Remove beginning1 + - tp_cat + - Grouping1 + - cat1 + - tp_head_tool + - Grep1 + - regex1 + update_time: '2023-11-10' + versions: 1 +- create_time: '2023-11-09' + creators: [] + doi: null + edam_operation: [] + edam_topic: + - Biodiversity + - Ecology + id: '659' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/659?version=1 + name: Animal dive prediction using deep learning + number_of_steps: 32 + source: WorkflowHub + tags: [] + tools: + - keras_model_config + - table_compute + - Remove beginning1 + - model_prediction + - keras_train_and_eval + - sklearn_fitted_model_eval + - sklearn_to_categorical + - cat1 + - keras_model_builder + - ml_visualization_ex + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Yvan Le Bras + - Pauline Seguineau + - Coline Royaux + doi: null + edam_operation: [] + edam_topic: + - Biodiversity + - Ecology + id: '658' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/658?version=1 + name: Ecoregionalization on Antarctic sea + number_of_steps: 5 + source: WorkflowHub + tags: [] + tools: + - ecoregion_eco_map + - ecoregion_cluster_estimate + - ecoregion_clara_cluster + - ecoregion_brt_analysis + - ecoregion_taxa_seeker + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Yvan Le Bras + - Coline Royaux + - "Marie Joss\xE9" + doi: null + edam_operation: [] + edam_topic: + - Biodiversity + - Ecology + - Environmental science + id: '657' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/657?version=1 + name: Remote sensing Sentinel 2 data analysis to produce biodiversity metrics + number_of_steps: 8 + source: WorkflowHub + tags: [] + tools: + - srs_diversity_maps + - srs_global_indices + - srs_spectral_indices + - srs_preprocess_s2 + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Yvan Le Bras + - Coline Royaux + - "Marie Joss\xE9" + doi: null + edam_operation: [] + edam_topic: + - Biodiversity + - Ecology + id: '656' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/656?version=1 + name: Biodiversity data exploration tutorial + number_of_steps: 6 + source: WorkflowHub + tags: [] + tools: + - ecology_stat_presence_abs + - ecology_link_between_var + - ecology_beta_diversity + - tool_anonymization + - ecology_homogeneity_normality + - ecology_presence_abs_abund + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Yvan Le Bras + - Coline Royaux + doi: null + edam_operation: + - Statistical calculation + - Sequence analysis + - Sequence composition calculation + - Sequencing quality control + edam_topic: + - Biodiversity + - Ecology + - Genetics + - Phylogenetics + id: '655' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/655?version=1 + name: Obitools eDNA metabarcoding + number_of_steps: 23 + source: WorkflowHub + tags: [] + tools: + - fastqc + - obi_uniq + - seq_filter_by_id + - unzip + - obi_tab + - Cut1 + - obi_clean + - obi_annotate + - join1 + - obi_stat + - wc_gnu + - obi_ngsfilter + - ncbi_blastn_wrapper + - obi_grep + - fastq_groomer + - obi_illumina_pairend + - Filter1 + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Saskia Hiltemann + - "B\xE9r\xE9nice Batut" + - Dave Clements + - Ahmed Mehdi + doi: null + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: '653' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/653?version=1 + name: 'Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]' + number_of_steps: 4 + source: WorkflowHub + tags: + - Metagenomics + tools: + - mothur_heatmap_sim + - newick_display + - mothur_tree_shared + - mothur_dist_shared + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Saskia Hiltemann + - "B\xE9r\xE9nice Batut" + - Dave Clements + - Ahmed Mehdi + doi: null + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: '652' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/652?version=1 + name: 'Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]' + number_of_steps: 3 + source: WorkflowHub + tags: + - Metagenomics + tools: + - mothur_summary_single + - XY_Plot_1 + - mothur_rarefaction_single + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Saskia Hiltemann + - "B\xE9r\xE9nice Batut" + - Dave Clements + - Ahmed Mehdi + doi: null + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: '651' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/651?version=1 + name: 'Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]' + number_of_steps: 5 + source: WorkflowHub + tags: + - Metagenomics + tools: + - mothur_count_groups + - mothur_cluster_split + - mothur_make_shared + - mothur_sub_sample + - mothur_classify_otu + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Saskia Hiltemann + - "B\xE9r\xE9nice Batut" + - Dave Clements + - Ahmed Mehdi + doi: null + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: '650' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/650?version=1 + name: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With + Mothur]' + number_of_steps: 2 + source: WorkflowHub + tags: + - Metagenomics + tools: + - mothur_classify_seqs + - mothur_remove_lineage + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Saskia Hiltemann + - "B\xE9r\xE9nice Batut" + - Dave Clements + - Ahmed Mehdi + doi: null + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: '648' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/648?version=1 + name: 'Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]' + number_of_steps: 5 + source: WorkflowHub + tags: + - Metagenomics + tools: + - mothur_screen_seqs + - mothur_unique_seqs + - mothur_summary_seqs + - mothur_count_seqs + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Saskia Hiltemann + - "B\xE9r\xE9nice Batut" + - Dave Clements + - Ahmed Mehdi + doi: null + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: '649' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/649?version=1 + name: 'Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With + Mothur]' + number_of_steps: 9 + source: WorkflowHub + tags: + - Metagenomics + tools: + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_remove_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_unique_seqs + - mothur_pre_cluster + update_time: '2023-11-09' + versions: 1 +- create_time: '2024-10-07' + creators: + - Delphine Lariviere + doi: null + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: '641' + latest_version: 13 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/641?version=13 + name: Assembly-Hifi-HiC-phasing-VGP4/main + number_of_steps: 32 + source: WorkflowHub + tags: + - Reviewed + - vgp + tools: + - '' + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2024-10-07' + versions: 13 +- create_time: '2023-10-11' + creators: + - Diego De Panis + doi: 10.48546/workflowhub.workflow.608.1 + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '608' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/608?version=1 + name: ERGA HiC Hap1Hap2 Scaffolding+QC YaHS v2309 (WF4) + number_of_steps: 30 + source: WorkflowHub + tags: + - Assembly+QC + - ERGA + - Hi-C + tools: + - bwa_mem2 + - yahs + - merqury + - pretext_snapshot + - gfastats + - pretext_map + - gfa_to_fa + - bellerophon + - param_value_from_file + - busco + update_time: '2024-03-13' + versions: 1 +- create_time: '2023-10-27' + creators: + - Wolfgang Maier + doi: 10.48546/workflowhub.workflow.629.1 + edam_operation: + - SNP annotation + edam_topic: + - Biomedical science + - Genetic variation + - Oncology + id: '629' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/629?version=1 + name: Cancer variant annotation (hg38 VEP-based) with MAF export + number_of_steps: 85 + source: WorkflowHub + tags: + - EOSC4Cancer + tools: + - tp_text_file_with_recurring_lines + - snpSift_filter + - snpSift_extractFields + - __EXTRACT_DATASET__ + - ensembl_vep + - collapse_dataset + - split_file_to_collection + - __RELABEL_FROM_FILE__ + - tp_tail_tool + - tp_replace_in_column + - tp_find_and_replace + - datamash_ops + - bcftools_plugin_split_vep + - compose_text_param + - export_remote + - __MERGE_COLLECTION__ + - vcfanno + - Add_a_column1 + - __SORTLIST__ + - __FILTER_FROM_FILE__ + - vcf2maf + - param_value_from_file + - __BUILD_LIST__ + - datamash_transpose + - Filter1 + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - tp_easyjoin_tool + update_time: '2023-10-27' + versions: 1 +- create_time: '2023-10-27' + creators: + - Wolfgang Maier + doi: 10.48546/workflowhub.workflow.628.1 + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: + - Biomedical science + - Genetic variation + - Oncology + id: '628' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/628?version=1 + name: Variant calling from matched tumor/normal sample pair (hg38 version) + number_of_steps: 47 + source: WorkflowHub + tags: + - EOSC4Cancer + tools: + - fastqc + - tp_text_file_with_recurring_lines + - trimmomatic + - __EXTRACT_DATASET__ + - split_file_to_collection + - collapse_dataset + - __RELABEL_FROM_FILE__ + - varscan_somatic + - Grep1 + - Convert characters1 + - compose_text_param + - samtools_calmd + - multiqc + - tp_replace_in_line + - samtools_rmdup + - qualimap_bamqc + - __APPLY_RULES__ + - __BUILD_LIST__ + - pick_value + - bwa_mem + - bamleftalign + - samtools_view + update_time: '2023-10-27' + versions: 1 +- create_time: '2024-07-02' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: null + edam_operation: + - Data handling + edam_topic: [] + id: '622' + latest_version: 11 + license: MIT + link: https://workflowhub.eu/workflows/622?version=11 + name: sra-manifest-to-concatenated-fastqs/main + number_of_steps: 13 + source: WorkflowHub + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-07-03' + versions: 11 +- create_time: '2024-06-01' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: '615' + latest_version: 5 + license: MIT + link: https://workflowhub.eu/workflows/615?version=5 + name: baredsc/baredSC-1d-logNorm + number_of_steps: 3 + source: WorkflowHub + tags: [] + tools: + - '' + - baredsc_1d + - baredsc_combine_1d + update_time: '2024-06-24' + versions: 5 +- create_time: '2024-06-22' + creators: + - Matthias Bernt + doi: null + edam_operation: [] + edam_topic: [] + id: '613' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/613?version=2 + name: openms-metaprosip/main + number_of_steps: 8 + source: WorkflowHub + tags: [] + tools: + - FalseDiscoveryRate + - FeatureFinderMultiplex + - IDMapper + - MSGFPlusAdapter + - DecoyDatabase + - MetaProSIP + - __SORTLIST__ + - PeptideIndexer + update_time: '2024-06-24' + versions: 2 +- create_time: '2023-10-10' + creators: + - Wolfgang Maier + doi: 10.48546/workflowhub.workflow.607.1 + edam_operation: + - SNP annotation + edam_topic: + - Biomedical science + - Genetic variation + - Oncology + id: '607' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/607?version=1 + name: Cancer variant annotation (hg38 VEP-based) + number_of_steps: 78 + source: WorkflowHub + tags: + - EOSC4Cancer + tools: + - tp_text_file_with_recurring_lines + - snpSift_filter + - snpSift_extractFields + - __EXTRACT_DATASET__ + - ensembl_vep + - collapse_dataset + - split_file_to_collection + - __RELABEL_FROM_FILE__ + - tp_replace_in_column + - tp_find_and_replace + - datamash_ops + - bcftools_plugin_split_vep + - __MERGE_COLLECTION__ + - vcfanno + - Add_a_column1 + - __SORTLIST__ + - __FILTER_FROM_FILE__ + - vcf2maf + - __BUILD_LIST__ + - datamash_transpose + - Filter1 + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - tp_easyjoin_tool + update_time: '2023-10-27' + versions: 1 +- create_time: '2023-10-09' + creators: + - Diego De Panis + doi: 10.48546/workflowhub.workflow.605.1 + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Transcriptome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: + - Whole genome sequencing + id: '605' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/605?version=1 + name: ERGA HiFi+HiC Assembly+QC Hifiasm v2309 (WF2) + number_of_steps: 21 + source: WorkflowHub + tags: + - Assembly+QC + - ERGA + - Hi-C + - HiFi + tools: + - hifiasm + - merqury + - gfastats + - gfa_to_fa + - bandage_image + - param_value_from_file + - busco + update_time: '2024-03-13' + versions: 1 +- create_time: '2023-06-28' + creators: + - Fabrice Touzain + doi: null + edam_operation: + - Data handling + - Genome indexing + - Read mapping + - Sequence contamination filtering + - Generation + - Sequence file editing + - Sequence alignment + - Sequencing quality control + edam_topic: + - Bioinformatics + id: '518' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/518?version=1 + name: VVV2_align_PE + number_of_steps: 10 + source: WorkflowHub + tags: + - Alignment + - Annotation + - Bioinformatics + - Galaxy + - SNPs + - Virus + - covid-19 + - paired-end + - variant calling + - variant_calling + - workflow + tools: + - fastp + - cshl_fasta_formatter + - vvv2_display + - seqtk_seq + - vadr + - vcfutils_vcf2fq + - vardict_java + - bcftools_call + - bcftools_mpileup + - bwa_mem + update_time: '2023-10-16' + versions: 1 +- create_time: '2023-06-27' + creators: + - Fabrice Touzain + doi: null + edam_operation: + - Data handling + - Genome indexing + - Read mapping + - Sequence contamination filtering + - Generation + - Sequence file editing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '517' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/517?version=1 + name: VVV2_align_SE + number_of_steps: 10 + source: WorkflowHub + tags: + - Annotation + - Bioinformatics + - Galaxy + - SNPs + - Virus + - high-throughput_sequencing_analysis + - single-end + - variant + - variant calling + - variant_calling + tools: + - fastp + - cshl_fasta_formatter + - vvv2_display + - seqtk_seq + - vadr + - vcfutils_vcf2fq + - vardict_java + - bcftools_call + - bcftools_mpileup + - bwa_mem + update_time: '2023-10-16' + versions: 1 +- create_time: '2023-10-04' + creators: + - Lucille Delisle + doi: null + edam_operation: [] + edam_topic: [] + id: '579' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/579?version=2 + name: average-bigwig-between-replicates/main + number_of_steps: 2 + source: WorkflowHub + tags: [] + tools: + - deeptools_bigwig_average + - __APPLY_RULES__ + update_time: '2024-06-13' + versions: 2 +- create_time: '2023-09-22' + creators: + - Romane Libouban + doi: null + edam_operation: + - Genome annotation + - Repeat sequence detection + edam_topic: [] + id: '575' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/575?version=1 + name: repeatmasking/main + number_of_steps: 2 + source: WorkflowHub + tags: [] + tools: + - repeatmasker_wrapper + - repeatmodeler + update_time: '2023-10-24' + versions: 1 +- create_time: '2023-09-08' + creators: + - Anna Syme + doi: null + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Mapping assembly + edam_topic: [] + id: '563' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/563?version=1 + name: polish-with-long-reads/main + number_of_steps: 8 + source: WorkflowHub + tags: [] + tools: + - minimap2 + - racon + update_time: '2024-04-20' + versions: 1 +- create_time: '2024-06-11' + creators: + - Marius van den Beek + doi: null + edam_operation: + - Data handling + edam_topic: [] + id: '137' + latest_version: 9 + license: MIT + link: https://workflowhub.eu/workflows/137?version=9 + name: parallel-accession-download/main + number_of_steps: 5 + source: WorkflowHub + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-06-11' + versions: 9 +- create_time: '2024-10-07' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: '561' + latest_version: 10 + license: MIT + link: https://workflowhub.eu/workflows/561?version=10 + name: consensus-peaks/consensus-peaks-chip-sr + number_of_steps: 17 + source: WorkflowHub + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-10-07' + versions: 10 +- create_time: '2024-10-07' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: '398' + latest_version: 13 + license: MIT + link: https://workflowhub.eu/workflows/398?version=13 + name: chipseq-pe/main + number_of_steps: 7 + source: WorkflowHub + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-10-07' + versions: 13 +- create_time: '2024-10-07' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: '397' + latest_version: 12 + license: MIT + link: https://workflowhub.eu/workflows/397?version=12 + name: chipseq-sr/main + number_of_steps: 7 + source: WorkflowHub + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-10-07' + versions: 12 +- create_time: '2023-08-11' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.558.1 + edam_operation: [] + edam_topic: [] + id: '558' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/558?version=1 + name: Galaxy Protein Conformational Transitions calculations tutorial + number_of_steps: 8 + source: WorkflowHub + tags: [] + tools: + - biobb_io_pdb_ext + - biobb_godmd_godmd_run_ext + - biobb_godmd_godmd_prep_ext + - biobb_structure_utils_extract_chain_ext + - biobb_analysis_cpptraj_convert_ext + - biobb_structure_utils_remove_molecules_ext + update_time: '2023-08-11' + versions: 1 +- create_time: '2023-08-11' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.557.1 + edam_operation: [] + edam_topic: [] + id: '557' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/557?version=1 + name: Galaxy Macromolecular Coarse-Grained Flexibility tutorial + number_of_steps: 27 + source: WorkflowHub + tags: [] + tools: + - biobb_analysis_cpptraj_rms_ext + - biobb_flexserv_pcz_bfactor_ext + - biobb_io_pdb_ext + - biobb_structure_utils_extract_atoms_ext + - biobb_flexserv_dmd_run_ext + - biobb_flexserv_pcz_zip_ext + - biobb_analysis_cpptraj_convert_ext + - biobb_flexserv_pcz_collectivity_ext + - biobb_flexserv_pcz_stiffness_ext + - biobb_flexserv_pcz_evecs_ext + - biobb_flexserv_pcz_info_ext + - biobb_flexserv_nma_run_ext + - biobb_flexserv_pcz_hinges_ext + - biobb_flexserv_bd_run_ext + - biobb_flexserv_pcz_unzip_ext + - biobb_flexserv_pcz_animate_ext + update_time: '2023-08-11' + versions: 1 +- create_time: '2023-06-28' + creators: + - Peter van Heusden + - Bradley W. Langhorst + doi: null + edam_operation: + - Genome alignment + - Read mapping + - Read binning + - Validation + - Sequence contamination filtering + - Sequence trimming + - RNA-Seq analysis + - SNP detection + - Filtering + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '519' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/519?version=1 + name: SARS-CoV-2 Illumina Amplicon pipeline - SANBI - v1.2 + number_of_steps: 20 + source: WorkflowHub + tags: + - ARTIC + - SANBI + - SARS-CoV-2 + - covid-19 + tools: + - fastp + - read_it_and_keep + - collapse_dataset + - tp_cat + - samtools_ampliconclip + - bbtools_bbmap + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - compose_text_param + - ivar_consensus + - tp_awk_tool + - samtools_view + - deeptools_bam_coverage + - multiqc + update_time: '2023-06-30' + versions: 1 +- create_time: '2023-06-29' + creators: [] + doi: null + edam_operation: + - Box-Whisker plot plotting + - Genome alignment + - Filtering + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: '521' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/521?version=1 + name: SARS-CoV-2 ONT Amplicon Sequencing SANBI 1.0 + number_of_steps: 5 + source: WorkflowHub + tags: + - SANBI + - SARS-CoV-2 + - nanopore + tools: + - artic_minion + - nanoplot + - read_it_and_keep + - artic_guppyplex + update_time: '2023-06-29' + versions: 1 +- create_time: '2023-06-28' + creators: [] + doi: null + edam_operation: + - Variant calling + - Genome visualisation + - Methylation analysis + edam_topic: [] + id: '520' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/520?version=1 + name: SARS-CoV-2 PostProcessing + number_of_steps: 2 + source: WorkflowHub + tags: + - SANBI + - SARS-CoV-2 + tools: + - jbrowse + - nextclade + update_time: '2023-06-28' + versions: 1 +- create_time: '2020-11-03' + creators: [] + doi: null + edam_operation: + - Parsing + - Image analysis + - Quantification + edam_topic: + - Bioimaging + - Imaging + id: '41' + latest_version: 2 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/41?version=2 + name: Nucleoli segmentation using CellProfiler (EOSC-Life D6) + number_of_steps: 25 + source: WorkflowHub + tags: + - CellProfiler + - Galaxy + - image processing + - imaging + tools: + - cp_measure_object_intensity + - cp_measure_object_size_shape + - cp_image_math + - cp_enhance_or_suppress_features + - cp_gray_to_color + - cp_convert_objects_to_image + - cp_mask_image + - cp_measure_texture + - idr_download_by_ids + - cp_measure_image_area_occupied + - cp_save_images + - cp_identify_primary_objects + - cp_cellprofiler + - cp_measure_image_quality + - cp_common + - cp_export_to_spreadsheet + - cp_measure_image_intensity + - cp_relate_objects + - cp_display_data_on_image + - cp_measure_granularity + update_time: '2023-07-03' + versions: 1 +- create_time: '2023-06-11' + creators: + - "Crist\xF3bal Gallardo" + doi: null + edam_operation: [] + edam_topic: + - Biomedical science + - Transcriptomics + id: '482' + latest_version: 7 + license: CC-BY-NC-4.0 + link: https://workflowhub.eu/workflows/482?version=7 + name: Genome-wide alternative splicing analysis v.2 + number_of_steps: 52 + source: WorkflowHub + tags: + - Alternative splicing + - Transcriptomics + - isoform switching + tools: [] + update_time: '2023-06-11' + versions: 7 +- create_time: '2023-06-01' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.490.1 + edam_operation: [] + edam_topic: [] + id: '490' + latest_version: 1 + license: other-open + link: https://workflowhub.eu/workflows/490?version=1 + name: Galaxy Protein conformational ensembles generation + number_of_steps: 43 + source: WorkflowHub + tags: [] + tools: + - biobb_flexserv_pcz_zip_ext + - biobb_analysis_cpptraj_mask_ext + - biobb_flexdyn_concoord_disco_ext + - biobb_flexserv_pcz_collectivity_ext + - biobb_flexdyn_nolb_nma_ext + - biobb_flexserv_pcz_evecs_ext + - biobb_analysis_gmx_cluster_ext + - biobb_flexserv_pcz_hinges_ext + - biobb_flexserv_bd_run_ext + - biobb_flexserv_dmd_run_ext + - zip + - biobb_structure_utils_extract_chain_ext + - biobb_flexdyn_imod_imc_ext + - biobb_analysis_cpptraj_convert_ext + - biobb_flexserv_pcz_info_ext + - biobb_analysis_cpptraj_rms_ext + - biobb_flexserv_pcz_bfactor_ext + - biobb_flexdyn_concoord_dist_ext + - biobb_flexdyn_prody_anm_ext + - biobb_flexdyn_imod_imode_ext + - biobb_gromacs_make_ndx_ext + - biobb_flexserv_pcz_animate_ext + - biobb_io_pdb_ext + - biobb_structure_utils_extract_model_ext + - biobb_flexserv_pcz_stiffness_ext + - biobb_flexserv_nma_run_ext + - biobb_gromacs_trjcat_ext + update_time: '2023-06-01' + versions: 1 +- create_time: '2023-05-25' + creators: + - "Crist\xF3bal Gallardo" + doi: null + edam_operation: [] + edam_topic: [] + id: '483' + latest_version: 1 + license: CC-BY-NC-4.0 + link: https://workflowhub.eu/workflows/483?version=1 + name: StringTie workflow + number_of_steps: 9 + source: WorkflowHub + tags: [] + tools: [] + update_time: '2023-05-25' + versions: 1 +- create_time: '2023-05-25' + creators: + - "Crist\xF3bal Gallardo" + doi: null + edam_operation: [] + edam_topic: + - Transcriptomics + id: '472' + latest_version: 4 + license: CC-BY-NC-4.0 + link: https://workflowhub.eu/workflows/472?version=4 + name: Genome-wide alternative splicing analysis + number_of_steps: 25 + source: WorkflowHub + tags: + - GTN + - Transcriptomics + - alternative-splicing + tools: [] + update_time: '2023-05-25' + versions: 4 +- create_time: '2023-05-03' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.299.3 + edam_operation: [] + edam_topic: [] + id: '299' + latest_version: 3 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/299?version=3 + name: Galaxy ABC MD Setup tutorial + number_of_steps: 26 + source: WorkflowHub + tags: [] + tools: + - "\n biobb_amber_process_minout_ext" + - "\n biobb_amber_cpptraj_randomize_ions_ext" + - "\n biobb_amber_process_mdout_ext" + - "\n biobb_amber_sander_mdrun_ext" + - "\n biobb_amber_leap_gen_top_ext" + - "\n biobb_amber_leap_solvate_ext" + - "\n biobb_amber_leap_add_ions_ext" + - "\n biobb_amber_parmed_hmassrepartition_ext" + update_time: '2023-05-03' + versions: 3 +- create_time: '2023-05-03' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.298.3 + edam_operation: [] + edam_topic: [] + id: '298' + latest_version: 3 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/298?version=3 + name: Galaxy Amber Protein Ligand Complex MD Setup tutorial + number_of_steps: 30 + source: WorkflowHub + tags: [] + tools: + - "\n biobb_structure_utils_remove_pdb_water_ext" + - "\n biobb_amber_process_minout_ext" + - "\n biobb_analysis_cpptraj_rgyr_ext" + - "\n biobb_structure_utils_remove_ligand_ext" + - "\n biobb_structure_utils_extract_heteroatoms_ext" + - "\n biobb_amber_sander_mdrun_ext" + - "\n biobb_io_pdb_ext" + - "\n biobb_amber_leap_gen_top_ext" + - "\n biobb_amber_amber_to_pdb_ext" + - "\n biobb_amber_pdb4amber_run_ext" + - "\n biobb_chemistry_babel_minimize_ext" + - "\n biobb_amber_leap_solvate_ext" + - "\n biobb_amber_leap_add_ions_ext" + - "\n biobb_chemistry_reduce_add_hydrogens_ext" + - "\n biobb_amber_process_mdout_ext" + - "\n biobb_analysis_cpptraj_rms_ext" + - "\n biobb_chemistry_acpype_params_ac_ext" + - "\n biobb_analysis_cpptraj_image_ext" + update_time: '2023-05-03' + versions: 3 +- create_time: '2023-05-03' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.297.3 + edam_operation: [] + edam_topic: [] + id: '297' + latest_version: 3 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/297?version=3 + name: Galaxy Amber Protein MD Setup tutorial + number_of_steps: 23 + source: WorkflowHub + tags: [] + tools: + - "\n biobb_amber_process_minout_ext" + - "\n biobb_analysis_cpptraj_rgyr_ext" + - "\n biobb_amber_sander_mdrun_ext" + - "\n biobb_io_pdb_ext" + - "\n biobb_amber_leap_gen_top_ext" + - "\n biobb_amber_amber_to_pdb_ext" + - "\n biobb_amber_pdb4amber_run_ext" + - "\n biobb_amber_leap_solvate_ext" + - "\n biobb_amber_leap_add_ions_ext" + - "\n biobb_amber_process_mdout_ext" + - "\n biobb_analysis_cpptraj_rms_ext" + - "\n biobb_analysis_cpptraj_image_ext" + update_time: '2023-05-03' + versions: 3 +- create_time: '2023-05-03' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.296.3 + edam_operation: [] + edam_topic: [] + id: '296' + latest_version: 3 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/296?version=3 + name: Galaxy Protein-ligand Docking tutorial (Fpocket) + number_of_steps: 14 + source: WorkflowHub + tags: [] + tools: + - "\n biobb_vs_fpocket_filter_ext" + - "\n biobb_vs_autodock_vina_run_ext" + - "\n biobb_vs_extract_model_pdbqt_ext" + - "\n biobb_structure_utils_extract_molecule_ext" + - "\n biobb_vs_box_ext" + - "\n biobb_io_pdb_ext" + - "\n biobb_structure_utils_cat_pdb_ext" + - "\n biobb_chemistry_babel_convert_ext" + - "\n biobb_vs_fpocket_run_ext" + - "\n biobb_structure_utils_str_check_add_hydrogens_ext" + - "\n biobb_vs_fpocket_select_ext" + - "\n biobb_io_ideal_sdf_ext" + update_time: '2023-05-03' + versions: 3 +- create_time: '2023-05-03' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.294.3 + edam_operation: [] + edam_topic: [] + id: '294' + latest_version: 3 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/294?version=3 + name: Galaxy GMX Automatic Ligand Parameterization tutorial + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: + - "\n biobb_chemistry_babel_minimize_ext" + - "\n biobb_io_ligand_ext" + - "\n biobb_chemistry_babel_add_hydrogens_ext" + - "\n biobb_chemistry_acpype_params_gmx_ext" + update_time: '2023-05-03' + versions: 3 +- create_time: '2023-05-03' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.277.3 + edam_operation: [] + edam_topic: [] + id: '277' + latest_version: 3 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/277?version=3 + name: Galaxy Protein MD Setup tutorial + number_of_steps: 23 + source: WorkflowHub + tags: [] + tools: + - "\n biobb_gromacs_pdb2gmx_ext" + - "\n biobb_analysis_gmx_rms_ext" + - "\n biobb_analysis_gmx_trjconv_str_ext" + - "\n biobb_gromacs_editconf_ext" + - "\n biobb_gromacs_solvate_ext" + - "\n biobb_io_pdb_ext" + - "\n biobb_analysis_gmx_rgyr_ext" + - "\n biobb_gromacs_mdrun_ext" + - "\n biobb_analysis_gmx_energy_ext" + - "\n biobb_analysis_gmx_image_ext" + - "\n biobb_gromacs_grompp_ext" + - "\n biobb_model_fix_side_chain_ext" + - "\n biobb_gromacs_genion_ext" + update_time: '2023-05-03' + versions: 3 +- create_time: '2023-03-01' + creators: + - Jasper Ouwerkerk + doi: 10.48546/workflowhub.workflow.363.2 + edam_operation: + - Sequence analysis + - Genetic variation analysis + edam_topic: [] + id: '363' + latest_version: 2 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/363?version=2 + name: Trio Analysis + number_of_steps: 12 + source: WorkflowHub + tags: + - variant-analysis + tools: + - pyega3 + - gemini_inheritance + - "\n Filter1" + - gemini_load + - regexColumn1 + - tp_grep_tool + - bcftools_norm + - bcftools_merge + - "\n CONVERTER_gz_to_uncompressed" + - snpEff + update_time: '2023-09-05' + versions: 2 +- create_time: '2024-06-22' + creators: + - Viktoria Isabel Schwarz + - Wolfgang Maier + doi: null + edam_operation: + - Sequence alignment analysis + - Local alignment + - Genome indexing + - Read mapping + - Global alignment + - Validation + - Sequence contamination filtering + - Sequence analysis + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '439' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/439?version=2 + name: pox-virus-amplicon/main + number_of_steps: 40 + source: WorkflowHub + tags: + - Virology + - pox + tools: + - 'EMBOSS: maskseq51' + - "\n Grep1" + - split_file_to_collection + - "\n __FILTER_FAILED_DATASETS__" + - samtools_stats + - "\n __SORTLIST__" + - fasta_compute_length + - collection_element_identifiers + - datamash_ops + - "\n __FLATTEN__" + - compose_text_param + - multiqc + - fastp + - ivar_trim + - "\n __APPLY_RULES__" + - "\n Cut1" + - samtools_merge + - tp_cat + - tp_sed_tool + - qualimap_bamqc + - bwa_mem + - "\n __ZIP_COLLECTION__" + - "\n param_value_from_file" + - ivar_consensus + - samtools_view + update_time: '2024-06-22' + versions: 2 +- create_time: '2023-02-17' + creators: + - Simon Bray + - Tim Dudgeon + doi: null + edam_operation: [] + edam_topic: [] + id: '246' + latest_version: 4 + license: MIT + link: https://workflowhub.eu/workflows/246?version=4 + name: fragment-based-docking-scoring/main + number_of_steps: 11 + source: WorkflowHub + tags: [] + tools: + - rxdock_rbcavity + - split_file_to_collection + - collapse_dataset + - ctb_frankenstein_ligand + - enumerate_charges + - compose_text_param + - rdock_sort_filter + - rxdock_rbdock + - sucos_docking_scoring + - openbabel_compound_convert + update_time: '2024-06-29' + versions: 4 +- create_time: '2021-02-04' + creators: [] + doi: null + edam_operation: + - Sequence contamination filtering + - Genome assembly + - Sequencing quality control + edam_topic: [] + id: '103' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/103?version=1 + name: '3: Plant virus exploration' + number_of_steps: 2 + source: WorkflowHub + tags: + - DE_NOVO + - Virology + - exploration + tools: + - shovill + - fastp + update_time: '2023-02-13' + versions: 1 +- create_time: '2021-02-04' + creators: [] + doi: null + edam_operation: + - Variant calling + - Sequence contamination filtering + - Formatting + - Pairwise sequence alignment + - Genome assembly + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: '102' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/102?version=1 + name: '2: Plant virus confirmation' + number_of_steps: 7 + source: WorkflowHub + tags: + - Assembly + - Virology + - blast + - mapping + - reads_selection + tools: + - ngsutils_bam_filter + - shovill + - fasta_merge_files_and_filter_unique_sequences + - samtools_stats + - picard_SamToFastq + - ncbi_blastn_wrapper + - minimap2 + update_time: '2023-02-13' + versions: 1 +- create_time: '2023-02-10' + creators: [] + doi: null + edam_operation: + - Data handling + - Genome assembly + edam_topic: [] + id: '434' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/434?version=1 + name: extract SRA + viralRNAspades (PE) + number_of_steps: 2 + source: WorkflowHub + tags: [] + tools: + - spades_rnaviralspades + - fasterq_dump + update_time: '2023-02-10' + versions: 1 +- create_time: '2024-10-07' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: '395' + latest_version: 14 + license: MIT + link: https://workflowhub.eu/workflows/395?version=14 + name: cutandrun/main + number_of_steps: 9 + source: WorkflowHub + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - "\n wig_to_bigWig" + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-10-07' + versions: 14 +- create_time: '2023-09-16' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: '420' + latest_version: 3 + license: MIT + link: https://workflowhub.eu/workflows/420?version=3 + name: hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler + number_of_steps: 4 + source: WorkflowHub + tags: + - Hi-C + tools: + - cooler_csort_tabix + - "\n " + - pygenomeTracks + update_time: '2024-10-17' + versions: 3 +- create_time: '2024-10-07' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: '399' + latest_version: 18 + license: MIT + link: https://workflowhub.eu/workflows/399?version=18 + name: atacseq/main + number_of_steps: 19 + source: WorkflowHub + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - "\n wig_to_bigWig" + - bamFilter + - "\n cat1" + - tp_grep_tool + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2024-10-07' + versions: 18 +- create_time: '2024-10-07' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '400' + latest_version: 9 + license: MIT + link: https://workflowhub.eu/workflows/400?version=9 + name: rnaseq-sr/main + number_of_steps: 19 + source: WorkflowHub + tags: + - RNASEQ + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - "\n wig_to_bigWig" + - bamFilter + - cutadapt + - tp_awk_tool + - compose_text_param + - "\n param_value_from_file" + - rna_star + - multiqc + update_time: '2024-10-07' + versions: 9 +- create_time: '2024-10-07' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '401' + latest_version: 10 + license: MIT + link: https://workflowhub.eu/workflows/401?version=10 + name: rnaseq-pe/main + number_of_steps: 20 + source: WorkflowHub + tags: + - RNASEQ + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - "\n wig_to_bigWig" + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - "\n param_value_from_file" + - rna_star + - multiqc + update_time: '2024-10-07' + versions: 10 +- create_time: '2022-12-14' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '413' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/413?version=1 + name: Mothra + number_of_steps: 2 + source: WorkflowHub + tags: [] + tools: + - "\n sdr_mothra" + - "\n save_output_rocrate" + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-12-06' + creators: + - "Kary Oca\xF1a" + doi: 10.48546/workflowhub.workflow.412.1 + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Read mapping + - Nucleic acid sequence analysis + edam_topic: [] + id: '412' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/412?version=1 + name: RNAseq_UMG_SDumont_v1 + number_of_steps: 8 + source: WorkflowHub + tags: [] + tools: + - "\n sort1" + - "\n Filter1" + - htseq_count + - bowtie2 + - deseq2 + update_time: '2023-02-13' + versions: 1 +- create_time: '2022-11-24' + creators: + - Saskia Hiltemann + - Willem de Koning + doi: null + edam_operation: + - Genome assembly + - De-novo assembly + - Aggregation + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Mapping assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: + - Microbiology + id: '406' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/406?version=1 + name: GTN Training - Antibiotic Resistance Detection + number_of_steps: 12 + source: WorkflowHub + tags: + - Metagenomics + tools: + - nanoplot + - staramr_search + - PlasFlow + - racon + - unicycler + - miniasm + - gfa_to_fa + - minimap2 + - bandage_image + update_time: '2023-02-13' + versions: 1 +- create_time: '2022-11-18' + creators: + - Yvan Le Bras + doi: null + edam_operation: [] + edam_topic: [] + id: '404' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/404?version=1 + name: GBIF data Quality check and filtering workflow Feb-2020 + number_of_steps: 11 + source: WorkflowHub + tags: [] + tools: + - "\n Count1" + - "\n Filter1" + - spocc_occ + - "\n Summary_Statistics1" + - gdal_ogr2ogr + update_time: '2023-11-09' + versions: 1 +- create_time: '2022-10-25' + creators: + - Wolfgang Maier + doi: null + edam_operation: + - Mapping + edam_topic: [] + id: '138' + latest_version: 5 + license: MIT + link: https://workflowhub.eu/workflows/138?version=5 + name: sars-cov-2-consensus-from-variation/COVID-19-CONSENSUS-CONSTRUCTION + number_of_steps: 17 + source: WorkflowHub + tags: + - covid-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - "\n Filter1" + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - collapse_dataset + - compose_text_param + - bcftools_consensus + update_time: '2024-01-14' + versions: 5 +- create_time: '2022-10-21' + creators: + - Gareth Price + - Katherine Farquharson + doi: 10.48546/workflowhub.workflow.221.3 + edam_operation: + - Sequence assembly visualisation + edam_topic: + - Sequence assembly + id: '221' + latest_version: 3 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/221?version=3 + name: PacBio HiFi genome assembly using hifiasm v2.1 + number_of_steps: 12 + source: WorkflowHub + tags: + - FASTQ + - HiFi + - genome_assembly + - hifiasm + tools: + - hifiasm + - bandage_info + - hifiadapterfilt + - fasta-stats + - gfa_to_fa + - bandage_image + update_time: '2023-01-30' + versions: 3 +- create_time: '2022-10-17' + creators: + - Gareth Price + doi: 10.48546/workflowhub.workflow.237.2 + edam_operation: + - Pairwise sequence alignment + - Read binning + - Scaffolding + - Genome assembly + edam_topic: + - Sequence assembly + id: '237' + latest_version: 2 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/237?version=2 + name: Purge duplicates from hifiasm assembly v1.0 + number_of_steps: 7 + source: WorkflowHub + tags: + - Assembly + - HiFi + - purge_dups + tools: + - minimap2 + - fasta-stats + - purge_dups + update_time: '2023-01-30' + versions: 2 +- create_time: '2022-10-17' + creators: + - Gareth Price + doi: 10.48546/workflowhub.workflow.220.2 + edam_operation: + - Sequence composition calculation + - Formatting + - Statistical calculation + - Sequencing quality control + edam_topic: + - Sequence assembly + id: '220' + latest_version: 2 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/220?version=2 + name: BAM to FASTQ + QC v1.0 + number_of_steps: 3 + source: WorkflowHub + tags: + - BAM + - Conversion + - FASTQ + - QC + tools: + - picard_SamToFastq + - fastqc + - samtools_flagstat + update_time: '2023-01-30' + versions: 2 +- create_time: '2022-10-15' + creators: + - Lucille Delisle + doi: null + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: '394' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/394?version=1 + name: ChIPseq_PE/main + number_of_steps: 7 + source: WorkflowHub + tags: + - ChIP + tools: + - "\n wig_to_bigWig" + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - bowtie2 + - samtool_filter2 + update_time: '2023-12-06' + versions: 1 +- create_time: '2022-07-29' + creators: + - Oliver Woolland + - Douglas Lowe + doi: null + edam_operation: [] + edam_topic: [] + id: '380' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/380?version=1 + name: Air Quality Prediction Prototype + number_of_steps: 9 + source: WorkflowHub + tags: [] + tools: + - "\n metgrid.cwl" + - "\n create_run_dir.cwl" + - "\n create_metgrid_dir.cwl" + - "\n wrf.cwl" + - "\n real.cwl" + - "\n link_grib_tool.cwl" + - "\n ungrib.cwl" + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-07-08' + creators: + - Laurence Livermore + - Oliver Woolland + doi: 10.48546/workflowhub.workflow.375.1 + edam_operation: [] + edam_topic: [] + id: '375' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/375?version=1 + name: HTR-Collections-test + number_of_steps: 8 + source: WorkflowHub + tags: + - Default-SDR + - collections + - multi-specimen-input + - validated-2022-06-29 + tools: + - "\n Remove beginning1" + - split_file_to_collection + - jq + - "\n __FILTER_FAILED_DATASETS__" + - bundle_collection + - "\n sdr_teklia_worker_htr" + - "\n sdr_teklia_worker_dla" + - "\n sdr_create_sdo_from_csv" + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-07-08' + creators: + - Laurence Livermore + - Oliver Woolland + doi: 10.48546/workflowhub.workflow.374.1 + edam_operation: [] + edam_topic: [] + id: '374' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/374?version=1 + name: DLA-Collections-test + number_of_steps: 7 + source: WorkflowHub + tags: + - Default-SDR + - collections + - multi-specimen-input + - validated-2022-06-29 + tools: + - "\n Remove beginning1" + - split_file_to_collection + - jq + - "\n __FILTER_FAILED_DATASETS__" + - bundle_collection + - "\n sdr_teklia_worker_dla" + - "\n sdr_create_sdo_from_csv" + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-12-14' + creators: + - Paul Brack + - Oliver Woolland + - Laurence Livermore + doi: null + edam_operation: [] + edam_topic: [] + id: '373' + latest_version: 2 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/373?version=2 + name: De novo digitisation + number_of_steps: 13 + source: WorkflowHub + tags: + - Default-SDR + tools: + - "\n Remove beginning1" + - split_file_to_collection + - jq + - "\n __FILTER_FAILED_DATASETS__" + - bundle_collection + - "\n sdr_teklia_worker_htr" + - "\n " + - "\n sdr_teklia_worker_dla" + - "\n sdr_create_sdo_from_csv" + - "\n sdr_teklia_worker_ner" + update_time: '2022-12-14' + versions: 2 +- create_time: '2022-06-14' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '366' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/366?version=1 + name: VGP-meryldb-creation/main + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: + - meryl + - genomescope + update_time: '2024-06-20' + versions: 1 +- create_time: '2022-06-14' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '365' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/365?version=1 + name: VGP-meryldb-creation-trio/main + number_of_steps: 12 + source: WorkflowHub + tags: [] + tools: + - meryl + - genomescope + - fastq_paired_end_interlacer + update_time: '2024-06-20' + versions: 1 +- create_time: '2022-06-12' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '364' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/364?version=1 + name: Workflow for running the Community Earth System Model in fully coupled mode + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-06-06' + creators: + - Miguel Roncoroni + doi: null + edam_operation: + - Phylogenetic analysis + - Sequence analysis + edam_topic: [] + id: '359' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/359?version=1 + name: ML phylogenetic reconstruction + number_of_steps: 5 + source: WorkflowHub + tags: + - phylogenetics + - phylogenomics + tools: + - astral + - iqtree + - phykit_alignment_based + - clipkit + update_time: '2023-02-13' + versions: 1 +- create_time: '2022-06-06' + creators: + - Miguel Roncoroni + doi: null + edam_operation: + - Genome assembly + - Scaffolding + - Genetic variation analysis + - Genome annotation + - Sequence analysis + - Transcriptome assembly + - Sequence clustering + - Multiple sequence alignment + - Sequence assembly validation + edam_topic: [] + id: '358' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/358?version=1 + name: preparing genomic data for phylogeny recostruction (GTN) + number_of_steps: 12 + source: WorkflowHub + tags: + - Annotation + - phylogenetics + - phylogenomics + tools: + - collapse_dataset + - tp_replace_in_line + - "\n Filter1" + - repeatmasker_wrapper + - proteinortho + - funannotate_predict + - proteinortho_grab_proteins + - clustalw + - busco + - glimmer_gbk_to_orf + - regex1 + update_time: '2023-02-13' + versions: 1 +- create_time: '2022-06-04' + creators: + - Anton Nekrutenko + doi: null + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '357' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/357?version=1 + name: generic-variant-calling-wgs-pe/main + number_of_steps: 12 + source: WorkflowHub + tags: + - generic + - mpxv + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-10-18' + versions: 1 +- create_time: '2022-06-03' + creators: + - Wolfgang Maier + doi: null + edam_operation: + - Mapping + edam_topic: + - Genetic variation + - Virology + id: '356' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/356?version=1 + name: Generic consensus construction from VCF calls + number_of_steps: 22 + source: WorkflowHub + tags: + - generic + - mlxv + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - "\n Filter1" + - bedtools_genomecoveragebed + - Add_a_column1 + - "\n Cut1" + - gops_merge_1 + - gops_subtract_1 + - collapse_dataset + - compose_text_param + - bcftools_consensus + update_time: '2023-02-13' + versions: 1 +- create_time: '2022-06-01' + creators: + - Wolfgang Maier + doi: null + edam_operation: [] + edam_topic: + - Genetic variation + - Virology + id: '354' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/354?version=1 + name: Generic variation analysis reporting + number_of_steps: 31 + source: WorkflowHub + tags: + - generic + - mpvx + tools: + - snpSift_filter + - snpSift_extractFields + - split_file_to_collection + - collapse_dataset + - Add_a_column1 + - "\n Filter1" + - "\n Cut1" + - datamash_ops + - tp_sort_header_tool + - tp_easyjoin_tool + - compose_text_param + - tp_find_and_replace + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-06-01' + creators: + - Wolfgang Maier + doi: null + edam_operation: + - Validation + - Sequence contamination filtering + - Formatting + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '353' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/353?version=1 + name: Generic variation analysis on WGS PE data + number_of_steps: 12 + source: WorkflowHub + tags: + - generic + - mpxv + tools: + - fastp + - lofreq_call + - lofreq_viterbi + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - multiqc + - bwa_mem + update_time: '2023-02-13' + versions: 1 +- create_time: '2022-05-31' + creators: + - Anna Syme + doi: null + edam_operation: [] + edam_topic: + - Population genomics + id: '352' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/352?version=1 + name: Partial ref-guided workflow - gstacks and pops + number_of_steps: 2 + source: WorkflowHub + tags: [] + tools: + - stacks2_populations + - stacks2_gstacks + update_time: '2023-01-30' + versions: 1 +- create_time: '2022-05-31' + creators: + - Anna Syme + doi: null + edam_operation: + - Validation + - Sequence alignment + - Sequencing quality control + edam_topic: + - Population genomics + id: '351' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/351?version=1 + name: Partial ref-guided workflow - bwa mem only + number_of_steps: 6 + source: WorkflowHub + tags: [] + tools: + - bwa_mem2 + - samtools_view + - samtools_stats + - multiqc + update_time: '2023-01-30' + versions: 1 +- create_time: '2022-05-31' + creators: + - Anna Syme + doi: null + edam_operation: [] + edam_topic: + - Population genomics + id: '350' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/350?version=1 + name: 'Partial de novo workflow: c-s-g-pops only' + number_of_steps: 5 + source: WorkflowHub + tags: [] + tools: + - stacks2_cstacks + - stacks2_populations + - stacks2_gstacks + - stacks2_sstacks + - stacks2_tsv2bam + update_time: '2023-01-30' + versions: 1 +- create_time: '2022-05-31' + creators: + - Anna Syme + doi: null + edam_operation: [] + edam_topic: + - Population genomics + id: '349' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/349?version=1 + name: 'Partial de novo workflow: ustacks only' + number_of_steps: 1 + source: WorkflowHub + tags: [] + tools: + - stacks2_ustacks + update_time: '2023-01-30' + versions: 1 +- create_time: '2022-05-31' + creators: + - Anna Syme + doi: null + edam_operation: [] + edam_topic: + - Population genomics + id: '348' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/348?version=1 + name: Stacks RAD-seq de novo workflow + number_of_steps: 6 + source: WorkflowHub + tags: [] + tools: + - stacks2_ustacks + - stacks2_cstacks + - stacks2_populations + - stacks2_gstacks + - stacks2_sstacks + - stacks2_tsv2bam + update_time: '2023-01-30' + versions: 1 +- create_time: '2022-05-31' + creators: + - Anna Syme + doi: null + edam_operation: + - Validation + - Sequence alignment + - Sequencing quality control + edam_topic: + - Population genomics + id: '347' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/347?version=1 + name: Stacks RAD-seq reference-guided workflow + number_of_steps: 8 + source: WorkflowHub + tags: [] + tools: + - bwa_mem2 + - stacks2_populations + - samtools_stats + - stacks2_gstacks + - samtools_view + - multiqc + update_time: '2023-01-30' + versions: 1 +- create_time: '2022-05-31' + creators: + - Anna Syme + doi: null + edam_operation: + - Validation + - Sequence contamination filtering + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: + - Population genomics + id: '346' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/346?version=1 + name: QC of RADseq reads + number_of_steps: 6 + source: WorkflowHub + tags: [] + tools: + - fastqc + - multiqc + - fastp + - cutadapt + update_time: '2023-01-30' + versions: 1 +- create_time: '2022-05-03' + creators: + - Marlene Rezk + doi: 10.48546/workflowhub.workflow.338.1 + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: '338' + latest_version: 1 + license: CC-BY-4.0 + link: https://workflowhub.eu/workflows/338?version=1 + name: Biomarker screening in preeclampsia + number_of_steps: 7 + source: WorkflowHub + tags: [] + tools: + - fastqc + - fastq_dump + - bowtie2 + - featurecounts + - deseq2 + update_time: '2023-02-13' + versions: 1 +- create_time: '2022-04-06' + creators: + - Delphine Lariviere + doi: null + edam_operation: [] + edam_topic: [] + id: '325' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/325?version=1 + name: VGP HiFi phased assembly with hifiasm and HiC data + number_of_steps: 23 + source: WorkflowHub + tags: + - Assembly + - Galaxy + - vgp + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-04-05' + creators: + - Delphine Lariviere + doi: null + edam_operation: [] + edam_topic: [] + id: '324' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/324?version=1 + name: VGP hybrid scaffolding with HiC data + number_of_steps: 19 + source: WorkflowHub + tags: + - Assembly + - Galaxy + - vgp + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-04-05' + creators: + - Delphine Lariviere + doi: null + edam_operation: [] + edam_topic: [] + id: '322' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/322?version=1 + name: VGP hybrid scaffolding with Bionano optical maps + number_of_steps: 6 + source: WorkflowHub + tags: + - Assembly + - Galaxy + - vgp + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-04-05' + creators: + - Delphine Lariviere + doi: null + edam_operation: [] + edam_topic: [] + id: '321' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/321?version=1 + name: VGP purge assembly with purge_dups pipeline + number_of_steps: 19 + source: WorkflowHub + tags: + - Assembly + - Galaxy + - vgp + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-04-05' + creators: + - Delphine Lariviere + doi: null + edam_operation: [] + edam_topic: [] + id: '318' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/318?version=1 + name: VGP HiFi phased assembly with hifiasm and HiC data + number_of_steps: 23 + source: WorkflowHub + tags: + - Assembly + - Galaxy + - vgp + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2022-04-05' + creators: + - Delphine Lariviere + doi: null + edam_operation: [] + edam_topic: [] + id: '309' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/309?version=1 + name: VGP genome profile analysis + number_of_steps: 6 + source: WorkflowHub + tags: + - Assembly + - Galaxy + - vgp + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2023-05-03' + creators: + - Adam Hospital + - "Gen\xEDs Bayarri" + doi: 10.48546/workflowhub.workflow.295.3 + edam_operation: [] + edam_topic: [] + id: '295' + latest_version: 3 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/295?version=3 + name: Galaxy Protein Ligand Complex MD Setup + number_of_steps: 35 + source: WorkflowHub + tags: [] + tools: + - "\n biobb_md_solvate_ext" + - "\n biobb_md_pdb2gmx_ext" + - "\n biobb_structure_utils_extract_molecule_ext" + - "\n biobb_md_genrestr_ext" + - "\n biobb_md_grompp_ext" + - "\n biobb_chemistry_acpype_params_gmx_ext" + - "\n biobb_structure_utils_cat_pdb_ext" + - "\n biobb_md_editconf_ext" + - "\n biobb_md_mdrun_ext" + - "\n biobb_analysis_gmx_energy_ext" + - "\n biobb_chemistry_reduce_add_hydrogens_ext" + - "\n biobb_model_fix_side_chain_ext" + - "\n biobb_md_genion_ext" + - "\n biobb_md_make_ndx_ext" + - "\n biobb_analysis_gmx_trjconv_str_ext" + - "\n biobb_structure_utils_extract_heteroatoms_ext" + - "\n biobb_io_pdb_ext" + - "\n biobb_analysis_gmx_rgyr_ext" + - "\n biobb_analysis_gmx_image_ext" + - "\n biobb_chemistry_babel_minimize_ext" + - "\n biobb_md_append_ligand_ext" + - "\n biobb_analysis_gmx_rms_ext" + update_time: '2023-05-03' + versions: 3 +- create_time: '2022-03-11' + creators: + - Anne Fouilloux + doi: 10.48546/workflowhub.workflow.274.1 + edam_operation: [] + edam_topic: [] + id: '274' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/274?version=1 + name: Galaxy workflow demonstrating the usage of EODIE Galaxy Tool + number_of_steps: 1 + source: WorkflowHub + tags: + - copernicus + - earth observation + - ndvi + - sentinel-2 data + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-09-26' + creators: [] + doi: 10.48546/workflowhub.workflow.194.1 + edam_operation: [] + edam_topic: [] + id: '194' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/194?version=1 + name: Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Galaxy + number_of_steps: 23 + source: WorkflowHub + tags: [] + tools: + - "Post-processing resulting 3D trajectory - part 5\n biobb_analysis_gmx_trjconv_str_ext" + - "Download a protein structure from the PDB database\n biobb_io_pdb_ext" + - "Energetically minimize the system - part 3\n biobb_analysis_gmx_energy_ext" + - "Equilibrate the system (NPT) - part 3\n biobb_analysis_gmx_energy_ext" + - "Fill the box with water molecules\n biobb_md_solvate_ext" + - "Free molecular dynamics simulation - part 2\n biobb_md_mdrun_ext" + - "Post-processing resulting 3D trajectory - part 2\n biobb_analysis_gmx_rms_ext" + - "Fix the side chains, adding any side chain atoms missing in the original structure\n\ + \ biobb_model_fix_side_chain_ext" + - "Free molecular dynamics simulation - part 1\n biobb_md_grompp_ext" + - "Add Ions - part 2\n biobb_md_genion_ext" + - "Energetically minimize the system - part 1\n biobb_md_grompp_ext" + - "Equilibrate the system (NVT) - part 2\n biobb_md_mdrun_ext" + - "Equilibrate the system (NPT) - part 1\n biobb_md_grompp_ext" + - "Create Solvent Box\n biobb_md_editconf_ext" + - "Post-processing resulting 3D trajectory - part 3\n biobb_analysis_gmx_rgyr_ext" + - "Post-processing resulting 3D trajectory - part 1\n biobb_analysis_gmx_rms_ext" + - "Equilibrate the system (NVT) - part 3\n biobb_analysis_gmx_energy_ext" + - "Post-processing resulting 3D trajectory - part 4\n biobb_analysis_gmx_image_ext" + - "Create Protein System Topology\n biobb_md_pdb2gmx_ext" + - "Equilibrate the system (NPT) - part 2\n biobb_md_mdrun_ext" + - "Energetically minimize the system - part 2\n biobb_md_mdrun_ext" + - "Add Ions - part 1\n biobb_md_grompp_ext" + - "Equilibriate the system (NVT) - part 1\n biobb_md_grompp_ext" + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-12-29' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '252' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/252?version=1 + name: Pangeo 101 for everyone - introduction to Xarray + number_of_steps: 40 + source: WorkflowHub + tags: + - Climate + - GTN + - copernicus + - pangeo + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-12-21' + creators: + - Simon Bray + doi: null + edam_operation: [] + edam_topic: [] + id: '249' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/249?version=2 + name: gromacs-dctmd/main + number_of_steps: 22 + source: WorkflowHub + tags: [] + tools: + - tp_text_file_with_recurring_lines + - split_file_to_collection + - add_line_to_file + - tp_cat + - gmx_sim + - biomd_neqgamma + - gmx_solvate + - tp_sed_tool + - gmx_makendx + - "\n d354bc62a13564f8" + - compose_text_param + - ctb_online_data_fetch + - "\n param_value_from_file" + - gmx_em + update_time: '2024-07-01' + versions: 2 +- create_time: '2021-12-21' + creators: + - Simon Bray + doi: null + edam_operation: [] + edam_topic: [] + id: '247' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/247?version=2 + name: protein-ligand-complex-parameterization/main + number_of_steps: 9 + source: WorkflowHub + tags: [] + tools: + - ambertools_acpype + - "\n Cut1" + - ctb_rdkit_descriptors + - gmx_setup + - tp_grep_tool + - "\n param_value_from_file" + - gmx_merge_topology_files + - ambertools_antechamber + - openbabel_compound_convert + update_time: '2024-07-01' + versions: 2 +- create_time: '2021-12-21' + creators: + - Wolfgang Maier + doi: null + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: '111' + latest_version: 5 + license: MIT + link: https://workflowhub.eu/workflows/111?version=5 + name: sars-cov-2-ont-artic-variant-calling/COVID-19-ARTIC-ONT + number_of_steps: 22 + source: WorkflowHub + tags: + - ARTIC + - ONT + - covid-19 + - covid19.galaxyproject.org + tools: + - "\n __FILTER_FAILED_DATASETS__" + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - "\n __FLATTEN__" + - lofreq_filter + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - bcftools_annotate + - bedtools_intersectbed + - "\n param_value_from_file" + - bamleftalign + - samtools_view + update_time: '2024-06-14' + versions: 5 +- create_time: '2021-12-21' + creators: + - Wolfgang Maier + doi: null + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: '112' + latest_version: 3 + license: MIT + link: https://workflowhub.eu/workflows/112?version=3 + name: sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA + number_of_steps: 9 + source: WorkflowHub + tags: + - covid-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2024-07-03' + versions: 3 +- create_time: '2021-12-21' + creators: + - Wolfgang Maier + doi: null + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '113' + latest_version: 4 + license: MIT + link: https://workflowhub.eu/workflows/113?version=4 + name: sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA + number_of_steps: 11 + source: WorkflowHub + tags: + - covid-19 + - covid19.galaxyproject.org + - emergen_validated + - iwc + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-06-29' + versions: 4 +- create_time: '2021-12-20' + creators: [] + doi: 10.48546/workflowhub.workflow.251.1 + edam_operation: [] + edam_topic: [] + id: '251' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/251?version=1 + name: Investigation of lockdown effect on air quality between January 2019 to May + 2021. + number_of_steps: 53 + source: WorkflowHub + tags: + - RELIANCE + - air-quality + - copernicus + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-11-26' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '245' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/245?version=1 + name: De novo digitisation + number_of_steps: 4 + source: WorkflowHub + tags: + - Segmentation + tools: + - jq + - "\n download_image" + - "\n sdr_create_sdo" + - "\n sdr_teklia_worker_dla" + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.230.1 + edam_operation: [] + edam_topic: [] + id: '230' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/230?version=1 + name: Combined workflows for large genome assembly + number_of_steps: 6 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - "\n 1fbcdce7d5823b15" + - "\n c0b5fbb61b12154d" + - "\n 2ed2445df255451a" + - "\n ec0fc1dbb6a13fe5" + - "\n ae3b48869cad659b" + - "\n 9d0e6aba18484ea8" + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-11-10' + creators: [] + doi: null + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Chimera detection + - Generation + - DNA mapping + - Sequence alignment + - Sequencing quality control + edam_topic: + - Metagenomics + id: '233' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/233?version=1 + name: 16S_biodiversity_for_nonoverlap_paired_end + number_of_steps: 25 + source: WorkflowHub + tags: + - MetaDEGalaxy + tools: + - fastqc + - vsearch_search + - trimmomatic + - vsearch_chimera_detection + - biom_convert + - phyloseq_net + - phyloseq_abundance + - phyloseq_DESeq2 + - picard_FilterSamReads + - vsearch_clustering + - phyloseq_richness + - "\n Cut1" + - "\n addValue" + - biom_add_metadata + - phyloseq_taxonomy + - bwa_mem + - samtools_fastx + - symmetricPlot + - vsearch_dereplication + - "\n cat1" + - uclust2otutable + - cat_multi_datasets + update_time: '2024-04-17' + versions: 1 +- create_time: '2021-11-10' + creators: [] + doi: null + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence merging + - Chimera detection + - Generation + - DNA mapping + - Sequence alignment + - Sequencing quality control + edam_topic: + - Metagenomics + id: '232' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/232?version=1 + name: 16S_biodiversity_for_overlap_paired_end + number_of_steps: 27 + source: WorkflowHub + tags: + - MetaDEGalaxy + tools: + - fastqc + - vsearch_search + - trimmomatic + - vsearch_chimera_detection + - biom_convert + - iuc_pear + - phyloseq_net + - phyloseq_abundance + - phyloseq_DESeq2 + - picard_FilterSamReads + - vsearch_clustering + - phyloseq_richness + - "\n Cut1" + - "\n addValue" + - biom_add_metadata + - phyloseq_taxonomy + - bwa_mem + - samtools_fastx + - symmetricPlot + - picard_MergeSamFiles + - "\n cat1" + - vsearch_dereplication + - uclust2otutable + update_time: '2024-04-17' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.229.1 + edam_operation: + - Scaffolding + - Visualisation + - Transcriptome assembly + - Genome assembly + - Sequence assembly validation + edam_topic: + - Sequence assembly + id: '229' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/229?version=1 + name: Assess genome quality + number_of_steps: 2 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - quast + - busco + update_time: '2023-01-30' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.227.1 + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Mapping assembly + edam_topic: + - Sequence assembly + id: '227' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/227?version=1 + name: Racon polish with long reads, x4 + number_of_steps: 8 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - minimap2 + - racon + update_time: '2023-01-30' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.225.1 + edam_operation: + - Visualisation + - Cross-assembly + - Mapping assembly + - Genome assembly + - De-novo assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: + - Sequence assembly + id: '225' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/225?version=1 + name: Assembly with Flye + number_of_steps: 5 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - quast + - flye + - fasta-stats + - "\n barchart_gnuplot" + - bandage_image + update_time: '2023-01-30' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.224.1 + edam_operation: + - Sequence contamination filtering + - Sequencing quality control + edam_topic: + - Sequence assembly + id: '224' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/224?version=1 + name: Trim and filter reads - fastp + number_of_steps: 2 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - fastp + update_time: '2023-01-30' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.223.1 + edam_operation: [] + edam_topic: + - Sequence assembly + id: '223' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/223?version=1 + name: kmer counting - meryl + number_of_steps: 3 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - meryl + - genomescope + update_time: '2023-01-30' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.222.1 + edam_operation: + - Validation + - Statistical calculation + - Scatter plot plotting + - Box-Whisker plot plotting + - Sequence composition calculation + - Sequencing quality control + edam_topic: + - Sequence assembly + id: '222' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/222?version=1 + name: Data QC + number_of_steps: 4 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - fastqc + - multiqc + - nanoplot + update_time: '2023-01-30' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.228.1 + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Mapping assembly + edam_topic: + - Sequence assembly + id: '228' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/228?version=1 + name: Racon polish with Illumina reads, x2 + number_of_steps: 4 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - minimap2 + - racon + update_time: '2023-01-30' + versions: 1 +- create_time: '2021-11-08' + creators: + - Anna Syme + doi: 10.48546/workflowhub.workflow.226.1 + edam_operation: + - Variant calling + - Sequence assembly + - Base-calling + edam_topic: + - Sequence assembly + id: '226' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/226?version=1 + name: Assembly polishing + number_of_steps: 6 + source: WorkflowHub + tags: + - Large-genome-assembly + tools: + - fasta-stats + - "\n 01041e6e0464607c" + - medaka_consensus_pipeline + - "\n d5a2cb013d9747c0" + update_time: '2023-01-30' + versions: 1 +- create_time: '2021-09-29' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '199' + latest_version: 1 + license: notspecified + link: https://workflowhub.eu/workflows/199?version=1 + name: lncRNA + number_of_steps: 12 + source: WorkflowHub + tags: [] + tools: + - "\n cbind" + - "\n d3f11f9fc62015d5" + - "\n cbind_fileList" + - "\n 1d3767f98cd53029" + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-09-26' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '193' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/193?version=1 + name: Workflow of BioTranslator Comparative Analysis + number_of_steps: 1 + source: WorkflowHub + tags: + - Pathway Analysis + - Semantic Comparison + - Semantic Network Analysis + tools: + - "The algorithm consists of two sequential tasks: \n\n1. Pathway Analysis of the\ + \ input gene sets, using the selected ontology \n2. Comparison of the derived\ + \ semantic sets, using the topology of ontological graph\n\nOutputs: \n1. The\ + \ distance matrix in tsv format\n2. A heatmap (png format) which illustrates the\ + \ agglomerative clustering of input sets, based on the respective semantic distances\n\ + \ comparative_analysis" + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-09-24' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '189' + latest_version: 3 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/189?version=3 + name: BioTranslator Workflow + number_of_steps: 1 + source: WorkflowHub + tags: + - Biomedical Ontologies + - Gene Prioritization + - Pathway Analysis + - Semantic Interpretation + - Semantic Network Analysis + tools: + - "The algorithm consists of two sequential tasks:\n1. Pathway Analysis, using the\ + \ selected ontology\n2. Gene Prioritization on the derived network of the enriched\ + \ terms\n\nOutputs:\n1. The enriched terms\n2. The highly prioritized input genes\n\ + 3. A heatmap which illustrates the association between prioritized genes and semantic\ + \ clusters\n biotranslator_lite" + update_time: '2023-01-16' + versions: 3 +- create_time: '2021-08-11' + creators: + - Mike Thang + doi: null + edam_operation: + - Formatting + edam_topic: + - Metagenomics + id: '142' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/142?version=1 + name: 16S_biodiversity_BIOM + number_of_steps: 8 + source: WorkflowHub + tags: + - MetaDEGalaxy + tools: + - phyloseq_DESeq2 + - symmetricPlot + - phyloseq_richness + - biom_convert + - biom_add_metadata + - phyloseq_taxonomy + - phyloseq_net + - phyloseq_abundance + update_time: '2024-04-17' + versions: 1 +- create_time: '2021-06-17' + creators: [] + doi: null + edam_operation: + - Visualisation + - Taxonomic classification + edam_topic: [] + id: '124' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/124?version=1 + name: '1: Plant virus detection with kraken2 (SE)' + number_of_steps: 3 + source: WorkflowHub + tags: + - Virology + - kraken + tools: + - kraken2 + - Kraken2Tax + - taxonomy_krona_chart + update_time: '2023-02-13' + versions: 1 +- create_time: '2021-02-04' + creators: [] + doi: null + edam_operation: + - Visualisation + - Taxonomic classification + edam_topic: [] + id: '101' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/101?version=1 + name: '1: Plant virus detection with kraken2 (PE)' + number_of_steps: 3 + source: WorkflowHub + tags: + - Virology + - kraken + tools: + - kraken2 + - Kraken2Tax + - taxonomy_krona_chart + update_time: '2023-02-13' + versions: 1 +- create_time: '2021-05-23' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '123' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/123?version=1 + name: Compute daily and monthly mean from meteorological station measurements + number_of_steps: 12 + source: WorkflowHub + tags: + - Climate + - eosc-nordic + - observation + tools: + - collection_column_join + - "\n Filter1" + - datamash_ops + - tp_awk_tool + - "\n barchart_gnuplot" + - "\n csv_to_tabular" + - climate_stripes + update_time: '2023-01-16' + versions: 1 +- create_time: '2021-04-09' + creators: + - Yvan Le Bras + doi: null + edam_operation: [] + edam_topic: [] + id: '117' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/117?version=1 + name: Workflow constructed from history 'test dwc from PNDB Data package EML DwC + annotations' + number_of_steps: 21 + source: WorkflowHub + tags: + - Darwin core + - Data package + - DataOne + - EML + - Ecological metadata language + - Galaxy + - Galaxy-E + - eml-annotation + tools: + - "\n Remove beginning1" + - "\n Grep1" + - filter_tabular + - regex_replace + - regexColumn1 + - tp_grep_tool + - tp_easyjoin_tool + - datamash_transpose + - bg_uniq + update_time: '2023-11-09' + versions: 1 +- create_time: '2021-03-21' + creators: [] + doi: null + edam_operation: + - Parsing + - Image analysis + - Quantification + edam_topic: + - Bioimaging + - Imaging + id: '115' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/115?version=1 + name: Object tracking using CellProfiler + number_of_steps: 12 + source: WorkflowHub + tags: + - CellProfiler + - Galaxy + - image processing + - imaging + tools: + - cp_measure_object_intensity + - cp_export_to_spreadsheet + - cp_measure_object_size_shape + - cp_overlay_outlines + - unzip + - cp_save_images + - cp_identify_primary_objects + - cp_cellprofiler + - cp_track_objects + - cp_color_to_gray + - cp_tile + - cp_common + update_time: '2023-07-03' + versions: 1 +- create_time: '2021-02-04' + creators: [] + doi: null + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - Format validation + - Variant calling + - Pairwise sequence alignment + - Sequence assembly + - Data retrieval + - Sequencing quality control + - Taxonomic classification + - Genome assembly + - Database search + - Sequence merging + - Sequence contamination filtering + - Visualisation + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Read pre-processing + edam_topic: [] + id: '100' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/100?version=1 + name: '0: View complete virus identification' + number_of_steps: 17 + source: WorkflowHub + tags: + - Virus + - exploration + - identification + tools: + - flash + - fastp + - Kraken2Tax + - taxonomy_krona_chart + - ncbi_tblastx_wrapper + - shovill + - ngsutils_bam_filter + - fasta_merge_files_and_filter_unique_sequences + - hmmer_hmmscan + - kraken2 + - picard_SamToFastq + - ncbi_blastn_wrapper + - minimap2 + update_time: '2023-02-13' + versions: 1 +- create_time: '2021-02-02' + creators: [] + doi: null + edam_operation: + - Sequence trimming + - Sequence alignment + - Genome indexing + - Generation + - Read pre-processing + - Read mapping + - Primer removal + edam_topic: [] + id: '99' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/99?version=1 + name: 'COVID-19: read pre-processing' + number_of_steps: 4 + source: WorkflowHub + tags: [] + tools: + - samtools_fastx + - trim_galore + - samtool_filter2 + - bwa_mem + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-11-04' + creators: [] + doi: null + edam_operation: + - Sequence contamination filtering + - Genome assembly + - Read mapping + - Aggregation + - Sequencing quality control + edam_topic: [] + id: '68' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/68?version=1 + name: MC_COVID19like_Assembly_Reads + number_of_steps: 7 + source: WorkflowHub + tags: + - covid-19 + tools: + - spades + - fastp + - unicycler + - bowtie2 + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-11-03' + creators: + - Pavankumar Videm + doi: null + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: '67' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/67?version=1 + name: RNA-RNA interactome analysis using CLAN + number_of_steps: 9 + source: WorkflowHub + tags: + - Transcriptomics + - rna + tools: + - fastqc + - chira_quantify + - chira_collapse + - query_tabular + - chira_extract + - cutadapt + - chira_map + - chira_merge + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-11-03' + creators: + - Pavankumar Videm + doi: null + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: '66' + latest_version: 1 + license: GPL-3.0 + link: https://workflowhub.eu/workflows/66?version=1 + name: RNA-RNA interactome analysis using BWA-MEM + number_of_steps: 9 + source: WorkflowHub + tags: + - Transcriptomics + - rna + tools: + - fastqc + - chira_quantify + - chira_collapse + - query_tabular + - chira_extract + - cutadapt + - chira_map + - chira_merge + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-10-27' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '65' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/65?version=1 + name: CLM-FATES_ALP1_simulation_5years + number_of_steps: 6 + source: WorkflowHub + tags: [] + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-08-05' + creators: + - Milad Miladi + doi: null + edam_operation: + - Visualisation + - Taxonomic classification + edam_topic: [] + id: '53' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/53?version=1 + name: ONT -- Metagenomics-Kraken2-Krona + number_of_steps: 4 + source: WorkflowHub + tags: + - ONT + tools: + - tp_replace_in_line + - kraken2 + - taxonomy_krona_chart + - datamash_reverse + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-08-05' + creators: + - Milad Miladi + doi: null + edam_operation: + - Sequence assembly visualisation + - Aggregation + - Genome assembly + edam_topic: [] + id: '52' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/52?version=1 + name: ONT - Workflow-Wick-et.al. + number_of_steps: 10 + source: WorkflowHub + tags: + - ONT + tools: + - bandage_image + - spades + - unicycler + - bandage_info + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-08-05' + creators: + - Milad Miladi + doi: null + edam_operation: + - Pairwise sequence alignment + - Cross-assembly + - Mapping assembly + - Genome assembly + - De-novo assembly + - Filtering + - Sequencing quality control + edam_topic: [] + id: '51' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/51?version=1 + name: ONT -- Assembly-Flye-AhrensLab + number_of_steps: 6 + source: WorkflowHub + tags: + - ONT + - name:ONT + tools: + - nanopolish_variants + - flye + - racon + - bam_to_sam + - filtlong + - minimap2 + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-08-05' + creators: + - Milad Miladi + doi: null + edam_operation: + - Pairwise sequence alignment + edam_topic: [] + id: '50' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/50?version=1 + name: ONT --Tutorial-Nanopolish-variants + number_of_steps: 2 + source: WorkflowHub + tags: [] + tools: + - minimap2 + - nanopolish_variants + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-07-24' + creators: + - Yvan Le Bras + - Coline Royaux + doi: null + edam_operation: [] + edam_topic: [] + id: '49' + latest_version: 2 + license: MIT + link: https://workflowhub.eu/workflows/49?version=2 + name: Population and community metrics calculation from Biodiversity data + number_of_steps: 4 + source: WorkflowHub + tags: + - Biodiversity + - Community_metrics + - Ecology + - GLM + - Modeling + - Presence_absence + - Species abundance + - Statistics + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-07-23' + creators: [] + doi: null + edam_operation: [] + edam_topic: [] + id: '46' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/46?version=1 + name: Copernicus Essential Climate Variable - select and plot + number_of_steps: 7 + source: WorkflowHub + tags: + - Climate + - Galaxy + - copernicus + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-06-29' + creators: + - Anne Fouilloux + doi: null + edam_operation: [] + edam_topic: [] + id: '42' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/42?version=1 + name: Climate - Climate 101 + number_of_steps: 13 + source: WorkflowHub + tags: + - Climate + - GTN + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-06-18' + creators: [] + doi: null + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - de Novo sequencing + - Format validation + - De-novo assembly + - Coding region prediction + - Differential gene expression analysis + - Sequence clustering + - Data retrieval + - Sequencing quality control + - Data handling + - Database search + - Sequence annotation + - Validation + - Sequence contamination filtering + - Conversion + - Probabilistic sequence generation + - Multiple sequence alignment + - Sequence generation + - Gene prediction + edam_topic: [] + id: '37' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/37?version=1 + name: Assembly using Tophat2 and annotation (alternate) + number_of_steps: 19 + source: WorkflowHub + tags: + - Alignment + - Assembly + - Galaxy + - RNASEQ + - Tophat2 + - covid-19 + tools: + - fastp + - gffread + - glimmer_build-icm + - hmmer_jackhmmer + - ncbi_blastp_wrapper + - glimmer_knowlegde-based + - cufflinks + - fasterq_dump + - antismash + - tophat2 + - cuffmerge + - transdecoder + - uniprotxml_downloader + - ncbi_makeblastdb + - multiqc + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-06-18' + creators: [] + doi: null + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - de Novo sequencing + - Format validation + - De-novo assembly + - Read mapping + - Aggregation + - Coding region prediction + - Differential gene expression analysis + - Sequence clustering + - Generation + - Data retrieval + - Sequencing quality control + - Data handling + - Genome assembly + - Genome indexing + - Database search + - Validation + - Sequence contamination filtering + - Gene prediction + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: '38' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/38?version=1 + name: Unicycler assembly and annotation + number_of_steps: 21 + source: WorkflowHub + tags: + - Alignment + - Annotation + - Assembly + - RNASEQ + - Unicycler + - covid-19 + tools: + - samtools_fastx + - fastp + - picard_MergeSamFiles + - glimmer_build-icm + - glimmer_knowlegde-based + - hmmer_jackhmmer + - ncbi_blastp_wrapper + - unicycler + - fasterq_dump + - antismash + - transdecoder + - uniprotxml_downloader + - ncbi_makeblastdb + - multiqc + - samtool_filter2 + - bwa_mem + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-06-18' + creators: [] + doi: null + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - de Novo sequencing + - Format validation + - De-novo assembly + - Read mapping + - Coding region prediction + - Differential gene expression analysis + - Sequence clustering + - Generation + - Data retrieval + - Sequencing quality control + - Data handling + - Genome indexing + - Database search + - Sequence annotation + - Validation + - Sequence contamination filtering + - RNA-Seq analysis + - Transcriptome assembly + - Gene prediction + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: '39' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/39?version=1 + name: StringTie assembly and annotation + number_of_steps: 22 + source: WorkflowHub + tags: + - Alignment + - Annotation + - Assembly + - RNASEQ + - StringTie + - covid-19 + tools: + - samtools_fastx + - fastp + - gffread + - glimmer_build-icm + - glimmer_knowlegde-based + - hmmer_jackhmmer + - ncbi_blastp_wrapper + - stringtie + - fasterq_dump + - antismash + - transdecoder + - hisat2 + - uniprotxml_downloader + - ncbi_makeblastdb + - multiqc + - stringtie_merge + - samtool_filter2 + - bwa_mem + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-06-18' + creators: [] + doi: null + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - de Novo sequencing + - Format validation + - De-novo assembly + - Read mapping + - Coding region prediction + - Differential gene expression analysis + - Sequence clustering + - Generation + - Data retrieval + - Sequencing quality control + - Data handling + - Genome indexing + - Database search + - Sequence annotation + - Validation + - Sequence contamination filtering + - Gene prediction + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: '40' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/40?version=1 + name: Assembly using Tophat2 and annotation + number_of_steps: 24 + source: WorkflowHub + tags: + - Alignment + - Annotation + - Assembly + - RNASEQ + - Tophat2 + - covid-19 + tools: + - glimmer_build-icm + - cuffquant + - cuffdiff + - fasterq_dump + - glimmer_knowlegde-based + - hmmer_jackhmmer + - cufflinks + - transdecoder + - uniprotxml_downloader + - multiqc + - fastp + - ncbi_blastp_wrapper + - antismash + - tophat2 + - ncbi_makeblastdb + - samtool_filter2 + - bwa_mem + - samtools_fastx + - gffread + - cuffmerge + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-06-18' + creators: [] + doi: null + edam_operation: + - Data handling + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '36' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/36?version=1 + name: 'COVID-19: VARSCAN' + number_of_steps: 19 + source: WorkflowHub + tags: + - Galaxy + - INDELs + - SNPs + - VARSCAN2 + tools: + - samtools_fastx + - vcfallelicprimitives + - fastp + - snpSift_extractFields + - samtools_sort + - varscan_mpileup + - fasterq_dump + - "\n cat1" + - snpEff_build_gb + - snpEff + - multiqc + - samtools_mpileup + - bowtie2 + - samtool_filter2 + - bwa_mem + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-06-18' + creators: [] + doi: null + edam_operation: + - Formatting + - Data handling + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: '35' + latest_version: 1 + license: Apache-2.0 + link: https://workflowhub.eu/workflows/35?version=1 + name: 'COVID-19: GATK4' + number_of_steps: 16 + source: WorkflowHub + tags: + - GATK4 + - Galaxy + - INDELs + - SNPs + tools: + - samtools_fastx + - vcfallelicprimitives + - fastp + - gatk4_mutect2 + - picard_SortSam + - snpSift_extractFields + - fasterq_dump + - picard_AddOrReplaceReadGroups + - "\n cat1" + - snpEff_build_gb + - snpEff + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + - bwa_mem + update_time: '2023-02-13' + versions: 1 +- create_time: '2020-05-29' + creators: + - Melchior du Lac + doi: null + edam_operation: [] + edam_topic: [] + id: '25' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/25?version=1 + name: Pathway Ranker + number_of_steps: 12 + source: WorkflowHub + tags: + - Retrosynthesis + - Synthetic Biology + - metabolic engineering + - pathway design + - pathway prediction + tools: + - "\n retrorules" + - "\n rp2paths" + - "\n rpThermo" + - "\n rpVisualiser" + - "\n retropath2" + - "\n rpReader" + - "\n makeSource" + - "\n rpCofactors" + - "\n rpReport" + - "\n rpFBA" + - "\n rpExtractSink" + - "\n rpGlobalScore" + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-05-29' + creators: + - Melchior du Lac + doi: null + edam_operation: [] + edam_topic: [] + id: '24' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/24?version=1 + name: RetroSynthesis + number_of_steps: 7 + source: WorkflowHub + tags: + - Retrosynthesis + - Synthetic Biology + - metabolic engineering + - pathway design + - pathway prediction + tools: + - "\n retrorules" + - "\n rp2paths" + - "\n retropath2" + - "\n rpReader" + - "\n makeSource" + - "\n rpCofactors" + - "\n rpExtractSink" + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-05-29' + creators: + - Melchior du Lac + doi: null + edam_operation: [] + edam_topic: [] + id: '23' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/23?version=1 + name: Genetic Design + number_of_steps: 7 + source: WorkflowHub + tags: + - Retrosynthesis + - genetic design + - pathway prediction + tools: + - "\n extractTaxonomy" + - "\n rpOptBioDes" + - "\n rpSelenzyme" + - "\n LCRGenie" + - "\n PartsGenie" + - "\n rpSBMLtoSBOL" + - "\n DNAWeaver" + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-05-29' + creators: + - Melchior du Lac + doi: null + edam_operation: [] + edam_topic: [] + id: '22' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/22?version=1 + name: Pathway Analysis + number_of_steps: 3 + source: WorkflowHub + tags: + - Retrosynthesis + tools: + - "\n rpGlobalScore" + - "\n rpThermo" + - "\n rpFBA" + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Tim Dudgeon + - ' Simon Bray' + - ' Gianmauro Cuccuru' + - " Bj\xF6rn Gr\xFCning" + - ' Rachael Skyner' + - ' Jack Scantlebury' + - ' Susan Leung' + - ' Frank von Delft' + doi: null + edam_operation: [] + edam_topic: [] + id: '18' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/18?version=1 + name: Cheminformatics - XChem combined + number_of_steps: 3 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Tim Dudgeon + - ' Simon Bray' + - ' Gianmauro Cuccuru' + - " Bj\xF6rn Gr\xFCning" + - ' Rachael Skyner' + - ' Jack Scantlebury' + - ' Susan Leung' + - ' Frank von Delft' + doi: null + edam_operation: [] + edam_topic: [] + id: '17' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/17?version=1 + name: Cheminformatics - Filter results + number_of_steps: 13 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Tim Dudgeon + - ' Simon Bray' + - ' Gianmauro Cuccuru' + - " Bj\xF6rn Gr\xFCning" + - ' Rachael Skyner' + - ' Jack Scantlebury' + - ' Susan Leung' + - ' Frank von Delft' + doi: null + edam_operation: [] + edam_topic: [] + id: '16' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/16?version=1 + name: Cheminformatics - TransFS scoring + number_of_steps: 3 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Tim Dudgeon + - ' Simon Bray' + - ' Gianmauro Cuccuru' + - " Bj\xF6rn Gr\xFCning" + - ' Rachael Skyner' + - ' Jack Scantlebury' + - ' Susan Leung' + - ' Frank von Delft' + doi: null + edam_operation: [] + edam_topic: [] + id: '15' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/15?version=1 + name: Cheminformatics - SuCOS scoring + number_of_steps: 5 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Tim Dudgeon + - ' Simon Bray' + - ' Gianmauro Cuccuru' + - " Bj\xF6rn Gr\xFCning" + - ' Rachael Skyner' + - ' Jack Scantlebury' + - ' Susan Leung' + - ' Frank von Delft' + doi: null + edam_operation: [] + edam_topic: [] + id: '14' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/14?version=1 + name: Cheminformatics - Docking + number_of_steps: 4 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Tim Dudgeon + - ' Simon Bray' + - ' Gianmauro Cuccuru' + - " Bj\xF6rn Gr\xFCning" + - ' Rachael Skyner' + - ' Jack Scantlebury' + - ' Susan Leung' + - ' Frank von Delft' + doi: null + edam_operation: [] + edam_topic: [] + id: '13' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/13?version=1 + name: Cheminformatics - Active site generation + number_of_steps: 2 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Tim Dudgeon + - ' Simon Bray' + - ' Gianmauro Cuccuru' + - " Bj\xF6rn Gr\xFCning" + - ' Rachael Skyner' + - ' Jack Scantlebury' + - ' Susan Leung' + - ' Frank von Delft' + doi: null + edam_operation: [] + edam_topic: [] + id: '12' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/12?version=1 + name: Cheminformatics - Enumerate ligands for docking + number_of_steps: 4 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Dannon Baker + - ' Marius van den Beek' + - ' Dave Bouvier' + - ' John Chilton' + - ' Nate Coraor' + - ' Frederik Coppens' + - ' Bert Droesbeke' + - ' Ignacio Eguinoa' + - ' Simon Gladman' + - " Bj\xF6rn Gr\xFCning" + - " Delphine Larivi\xE8re" + - " Gildas Le Corguill\xE9" + - ' Andrew Lonie' + - ' Nicholas Keener' + - ' Sergei Kosakovsky Pond' + - ' Wolfgang Maier' + - ' Anton Nekrutenko' + - ' James Taylor' + - ' Steven Weaver' + doi: null + edam_operation: [] + edam_topic: [] + id: '10' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/10?version=1 + name: Genomics - Recombination and selection analysis + number_of_steps: 6 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Dannon Baker + - ' Marius van den Beek' + - ' Dave Bouvier' + - ' John Chilton' + - ' Nate Coraor' + - ' Frederik Coppens' + - ' Bert Droesbeke' + - ' Ignacio Eguinoa' + - ' Simon Gladman' + - " Bj\xF6rn Gr\xFCning" + - " Delphine Larivi\xE8re" + - " Gildas Le Corguill\xE9" + - ' Andrew Lonie' + - ' Nicholas Keener' + - ' Sergei Kosakovsky Pond' + - ' Wolfgang Maier' + - ' Anton Nekrutenko' + - ' James Taylor' + - ' Steven Weaver' + doi: null + edam_operation: [] + edam_topic: [] + id: '9' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/9?version=1 + name: Genomics - Analysis of S-protein polymorphism + number_of_steps: 3 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Dannon Baker + - ' Marius van den Beek' + - ' Dave Bouvier' + - ' John Chilton' + - ' Nate Coraor' + - ' Frederik Coppens' + - ' Bert Droesbeke' + - ' Ignacio Eguinoa' + - ' Simon Gladman' + - " Bj\xF6rn Gr\xFCning" + - " Delphine Larivi\xE8re" + - " Gildas Le Corguill\xE9" + - ' Andrew Lonie' + - ' Nicholas Keener' + - ' Sergei Kosakovsky Pond' + - ' Wolfgang Maier' + - ' Anton Nekrutenko' + - ' James Taylor' + - ' Steven Weaver' + doi: null + edam_operation: [] + edam_topic: [] + id: '8' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/8?version=1 + name: Genomics - SE Variation + number_of_steps: 12 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Dannon Baker + - ' Marius van den Beek' + - ' Dave Bouvier' + - ' John Chilton' + - ' Nate Coraor' + - ' Frederik Coppens' + - ' Bert Droesbeke' + - ' Ignacio Eguinoa' + - ' Simon Gladman' + - " Bj\xF6rn Gr\xFCning" + - " Delphine Larivi\xE8re" + - " Gildas Le Corguill\xE9" + - ' Andrew Lonie' + - ' Nicholas Keener' + - ' Sergei Kosakovsky Pond' + - ' Wolfgang Maier' + - ' Anton Nekrutenko' + - ' James Taylor' + - ' Steven Weaver' + doi: null + edam_operation: [] + edam_topic: [] + id: '7' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/7?version=1 + name: Genomics - PE Variation + number_of_steps: 14 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-05-30' + versions: 1 +- create_time: '2020-04-10' + creators: + - Dannon Baker + - ' Marius van den Beek' + - ' Dave Bouvier' + - ' John Chilton' + - ' Nate Coraor' + - ' Frederik Coppens' + - ' Bert Droesbeke' + - ' Ignacio Eguinoa' + - ' Simon Gladman' + - " Bj\xF6rn Gr\xFCning" + - " Delphine Larivi\xE8re" + - " Gildas Le Corguill\xE9" + - ' Andrew Lonie' + - ' Nicholas Keener' + - ' Sergei Kosakovsky Pond' + - ' Wolfgang Maier' + - ' Anton Nekrutenko' + - ' James Taylor' + - ' Steven Weaver' + doi: null + edam_operation: [] + edam_topic: [] + id: '6' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/6?version=1 + name: Genomics - MRCA analysis + number_of_steps: 9 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Dannon Baker + - ' Marius van den Beek' + - ' Dave Bouvier' + - ' John Chilton' + - ' Nate Coraor' + - ' Frederik Coppens' + - ' Bert Droesbeke' + - ' Ignacio Eguinoa' + - ' Simon Gladman' + - " Bj\xF6rn Gr\xFCning" + - " Delphine Larivi\xE8re" + - " Gildas Le Corguill\xE9" + - ' Andrew Lonie' + - ' Nicholas Keener' + - ' Sergei Kosakovsky Pond' + - ' Wolfgang Maier' + - ' Anton Nekrutenko' + - ' James Taylor' + - ' Steven Weaver' + doi: null + edam_operation: [] + edam_topic: [] + id: '5' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/5?version=1 + name: Genomics - Assembly of the genome sequence + number_of_steps: 6 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Dannon Baker + - ' Marius van den Beek' + - ' Dave Bouvier' + - ' John Chilton' + - ' Nate Coraor' + - ' Frederik Coppens' + - ' Bert Droesbeke' + - ' Ignacio Eguinoa' + - ' Simon Gladman' + - " Bj\xF6rn Gr\xFCning" + - " Delphine Larivi\xE8re" + - " Gildas Le Corguill\xE9" + - ' Andrew Lonie' + - ' Nicholas Keener' + - ' Sergei Kosakovsky Pond' + - ' Wolfgang Maier' + - ' Anton Nekrutenko' + - ' James Taylor' + - ' Steven Weaver' + doi: null + edam_operation: [] + edam_topic: [] + id: '4' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/4?version=1 + name: Genomics - Read pre-processing without downloading from SRA + number_of_steps: 13 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2020-04-10' + creators: + - Dannon Baker + - ' Marius van den Beek' + - ' Dave Bouvier' + - ' John Chilton' + - ' Nate Coraor' + - ' Frederik Coppens' + - ' Bert Droesbeke' + - ' Ignacio Eguinoa' + - ' Simon Gladman' + - " Bj\xF6rn Gr\xFCning" + - " Delphine Larivi\xE8re" + - " Gildas Le Corguill\xE9" + - ' Andrew Lonie' + - ' Nicholas Keener' + - ' Sergei Kosakovsky Pond' + - ' Wolfgang Maier' + - ' Anton Nekrutenko' + - ' James Taylor' + - ' Steven Weaver' + doi: null + edam_operation: [] + edam_topic: [] + id: '2' + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/2?version=1 + name: Genomics - Read pre-processing + number_of_steps: 15 + source: WorkflowHub + tags: + - covid-19 + tools: [] + update_time: '2023-01-16' + versions: 1 +- create_time: '2024-09-30' + creators: + - droc + doi: '' + edam_operation: [] + edam_topic: [] + id: c44199b6217bdabe + latest_version: 1 + license: AGPL-3.0-or-later + link: https://usegalaxy.fr/published/workflow?id=c44199b6217bdabe + name: TraceAncestor + number_of_steps: null + source: https://usegalaxy.fr + tags: + - VCF + - Chromosomepainting + - Phylogenomics + tools: + - prefilter + - traceancestor + - vcf2gst + update_time: '2024-10-01' + versions: 1 +- create_time: '2024-06-05' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 192ff9aa79217899 + latest_version: 0 + license: null + link: https://usegalaxy.fr/published/workflow?id=192ff9aa79217899 + name: Workflow GC-MS_ESR_10_Exp_1 + number_of_steps: null + source: https://usegalaxy.fr + tags: + - GC-MS + - Metabolomics + - '2024' + tools: + - xcms_merge + - abims_xcms_group + - metams_runGC + - abims_xcms_xcmsSet + - msnbase_readmsdata + update_time: '2024-08-03' + versions: 0 +- create_time: '2022-06-14' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + edam_topic: [] + id: 048cb90ec1ac7120 + latest_version: 3 + license: null + link: https://usegalaxy.fr/published/workflow?id=048cb90ec1ac7120 + name: Workflow MiSeq 16S Bactos + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - FROGS_biom_to_tsv + - FROGS_OTU_filters + - FROGS_clustering + - FROGS_preprocess + - FROGS_remove_chimera + - FROGS_clusters_stat + update_time: '2024-07-31' + versions: 3 +- create_time: '2024-07-12' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 98bb6a831a2b399d + latest_version: 2 + license: null + link: https://usegalaxy.fr/published/workflow?id=98bb6a831a2b399d + name: Workflow pretreatment Data Beloukha July-2024 + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - xcms_merge + - abims_xcms_fillPeaks + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + update_time: '2024-07-12' + versions: 2 +- create_time: '2024-03-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7ae6ad6f74a50fac + latest_version: 6 + license: null + link: https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac + name: Fluxomics_Workflow_Beta_v0.1 + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - physiofit + - isoplot + - influx_data_manager + - influx_si + - physiofit_data_manager + - isocor + update_time: '2024-07-12' + versions: 6 +- create_time: '2024-05-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 879408d684923861 + latest_version: 5 + license: null + link: https://usegalaxy.fr/published/workflow?id=879408d684923861 + name: Workflow constructed from history 'ISOCOR_TRACEGROOMER_DIMET' + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - dimet_timecourse_analysis + - dimet_differential_multigroup_analysis + - tracegroomer + - dimet_pca_analysis + - dimet_isotopologues_plot + - dimet_pca_plot + - dimet_differential_analysis + - dimet_abundance_plot + - dimet_metabologram + - dimet_enrichment_plot + - dimet_bivariate_analysis + - isocor + update_time: '2024-05-31' + versions: 5 +- create_time: '2022-11-21' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 65ab28829a1f9803 + latest_version: 9 + license: null + link: https://usegalaxy.fr/published/workflow?id=65ab28829a1f9803 + name: ABiMS - Galaxy initiation - Find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2024-05-27' + versions: 9 +- create_time: '2024-05-13' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 49e59327f299e9f7 + latest_version: 6 + license: null + link: https://usegalaxy.fr/published/workflow?id=49e59327f299e9f7 + name: peakpicking-group + number_of_steps: null + source: https://usegalaxy.fr + tags: + - '2024' + - EBI_course + - LCMS + - MTBLS719 + tools: + - xcms_merge + - abims_xcms_xcmsSet + - abims_xcms_group + update_time: '2024-05-17' + versions: 6 +- create_time: '2023-01-19' + creators: + - Coline Royaux + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Data handling + - Sequence file editing + - Demultiplexing + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 41264142d3c00016 + latest_version: 33 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=41264142d3c00016 + name: 'Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST' + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - cshl_fastx_reverse_complement + - aligned_to_consensus + - filter_by_fasta_ids + - mothur_degap_seqs + - __SORTLIST__ + - fastq_to_tabular + - tab2fasta + - seqtk_mergepe + - ab1_fastq_converter + - seqtk_trimfq + - mothur_merge_files + - qiime_align_seqs + - fastq_groomer + - ncbi_blastn_wrapper + - regex1 + update_time: '2024-05-06' + versions: 33 +- create_time: '2024-03-13' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - Format validation + - Database search + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Data retrieval + edam_topic: [] + id: 7ebb54181b404733 + latest_version: 3 + license: null + link: https://usegalaxy.fr/published/workflow?id=7ebb54181b404733 + name: Genfam_introgrice_cds_33_species + number_of_steps: null + source: https://usegalaxy.fr + tags: + - gene + - family + - cds + tools: + - hmm2fasta + - rbc_mafft + - tp_cat + - hmmsearch_db + - hmmer_hmmbuild + - trimal + update_time: '2024-04-14' + versions: 3 +- create_time: '2024-04-02' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: aa96487c5a1b29bf + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=aa96487c5a1b29bf + name: Workflow constructed from history 'Copy of 'Copy of 'DataDrozo_RAEG2024''' + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - multiqc + - stringtie + - hisat2 + update_time: '2024-04-02' + versions: 1 +- create_time: '2024-03-26' + creators: + - Romane Libouban + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - Scaffolding + - Sequence analysis + - Transcriptome assembly + - Genome annotation + - Gene prediction + - Sequence assembly validation + edam_topic: [] + id: 2c823ac083c3cb6d + latest_version: 4 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=2c823ac083c3cb6d + name: Training - Helixer + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - compleasm + - helixer + - jcvi_gff_stats + - jbrowse + - busco + update_time: '2024-03-27' + versions: 4 +- create_time: '2024-02-23' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - Scaffolding + - Sequence analysis + - Transcriptome assembly + - Genome annotation + - RNA-Seq analysis + - Gene prediction + - Editing + - Sequence assembly validation + edam_topic: [] + id: 55be36ab73515e65 + latest_version: 20 + license: null + link: https://usegalaxy.fr/published/workflow?id=55be36ab73515e65 + name: Helixer and RED - annotation + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - compleasm + - helixer + - jcvi_gff_stats + - red + - jbrowse + - busco + update_time: '2024-03-26' + versions: 20 +- create_time: '2024-02-28' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - Scaffolding + - Sequence analysis + - Transcriptome assembly + - Genome annotation + - Repeat sequence detection + - Gene prediction + - Sequence assembly validation + edam_topic: [] + id: ae05ff8487f58fd6 + latest_version: 14 + license: null + link: https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6 + name: Helixer and RepeatModeler - annotation + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - compleasm + - helixer + - jcvi_gff_stats + - repeatmasker_wrapper + - jbrowse + - repeatmodeler + - busco + update_time: '2024-03-26' + versions: 14 +- create_time: '2024-02-07' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Data handling + - Read mapping + - Nucleic acid sequence analysis + edam_topic: [] + id: ff14dc4005e92cfd + latest_version: 4 + license: null + link: https://usegalaxy.fr/published/workflow?id=ff14dc4005e92cfd + name: Workflow differential analysis + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - deseq2 + - bowtie2 + - fasterq_dump + - htseq_count + update_time: '2024-03-06' + versions: 4 +- create_time: '2024-02-26' + creators: + - Maximilian Stingl + doi: '' + edam_operation: [] + edam_topic: [] + id: 5083dccc00274ac1 + latest_version: 7 + license: null + link: https://usegalaxy.fr/published/workflow?id=5083dccc00274ac1 + name: 'met4j workflow for GOLIATH: subnetwork extraction from metabolite list' + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - Cut1 + - met4j_ExtractSubBipNetwork + - tp_cat + - Grep1 + - tp_sorted_uniq + update_time: '2024-03-04' + versions: 7 +- create_time: '2024-02-29' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: b6311795ae10032b + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=b6311795ae10032b + name: Workflow constructed from history 'Data_Beloukha_Ctr_For_QC_BK_24_02_2024' + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - xcms_merge + - abims_xcms_fillPeaks + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + update_time: '2024-02-29' + versions: 1 +- create_time: '2024-01-29' + creators: + - Pierre + - abromics-consortium + - Abromics + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Expression analysis + - Statistical calculation + - Taxonomic classification + - Cross-assembly + edam_topic: [] + id: 3d3b40398d1cd1ae + latest_version: 8 + license: GPL-3.0-or-later + link: https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae + name: Checking expected species and contamination in bacterial isolate + number_of_steps: null + source: https://usegalaxy.fr + tags: + - ecology + tools: + - recentrifuge + - kraken2 + - est_abundance + update_time: '2024-01-29' + versions: 8 +- create_time: '2024-01-25' + creators: + - "B\xE9r\xE9nice Batut" + - Pierre Marin + doi: '' + edam_operation: + - Genome annotation + - Protein feature detection + - Genome assembly + - Nucleic acid feature detection + - Structural variation detection + - Sequence motif recognition + - Scaffolding + - Multilocus sequence typing + edam_topic: [] + id: 7964ddc68853458f + latest_version: 6 + license: GPL-3.0-or-later + link: https://usegalaxy.fr/published/workflow?id=7964ddc68853458f + name: Bacterial genome annotation + number_of_steps: null + source: https://usegalaxy.fr + tags: + - genome-annotation + tools: + - plasmidfinder + - integron_finder + - bakta + - isescan + update_time: '2024-01-25' + versions: 6 +- create_time: '2024-01-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 334189184455d9a2 + latest_version: 0 + license: null + link: https://usegalaxy.fr/published/workflow?id=334189184455d9a2 + name: qc_mapping_rna-seq + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - stringtie + - bamFilter + - sickle + - wig_to_bigWig + - rseqc_bam2wig + - hisat2 + update_time: '2024-01-18' + versions: 0 +- create_time: '2023-12-12' + creators: + - Coline Royaux + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Data handling + - Sequence file editing + - Demultiplexing + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 8b1678200a1d157a + latest_version: 7 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a + name: Training Sanger sequences CHD8 + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - cshl_fastx_reverse_complement + - collection_element_identifiers + - unzip + - filter_by_fasta_ids + - aligned_to_consensus + - mothur_degap_seqs + - __SORTLIST__ + - fastq_to_tabular + - tab2fasta + - __FILTER_FROM_FILE__ + - ab1_fastq_converter + - seqtk_trimfq + - seqtk_mergepe + - qiime_align_seqs + - fastq_groomer + - mothur_merge_files + - ncbi_blastn_wrapper + - regex1 + update_time: '2023-12-19' + versions: 7 +- create_time: '2023-11-22' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + edam_topic: [] + id: 63b49f322ec366b5 + latest_version: 2 + license: null + link: https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5 + name: Genfam_wf_2.2_cds_phylogeny + number_of_steps: null + source: https://usegalaxy.fr + tags: + - gene + - tree + - nucleic + tools: + - rbc_mafft + - fastatophylip + - RapGreen + - phyml + - trimal + update_time: '2023-11-22' + versions: 2 +- create_time: '2023-11-22' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - Format validation + - Database search + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Data retrieval + edam_topic: [] + id: 5ec6d378e60f7ccc + latest_version: 5 + license: null + link: https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc + name: Genfam_introgrice_wf_1.1_prot_build_13_species + number_of_steps: null + source: https://usegalaxy.fr + tags: + - gene + - family + - polypeptide + tools: + - hmm2fasta + - rbc_mafft + - tp_cat + - hmmsearch_db + - hmmer_hmmbuild + - trimal + update_time: '2023-11-22' + versions: 5 +- create_time: '2023-11-22' + creators: + - "Saliha ZENBOUDJI, St\xE9phanie BOCS, Ga\xEBtan DROC" + doi: '' + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - Format validation + - Database search + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Data retrieval + edam_topic: [] + id: d425a77157cae2ee + latest_version: 2 + license: null + link: https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee + name: Genfam_introgrice_wf_2.1_cds_build_6_species + number_of_steps: null + source: https://usegalaxy.fr + tags: + - gene + - family + - cds + tools: + - hmm2fasta + - rbc_mafft + - tp_cat + - hmmsearch_db + - hmmer_hmmbuild + - trimal + update_time: '2023-11-22' + versions: 2 +- create_time: '2023-11-22' + creators: + - "Saliha ZENBOUDJI, St\xE9phanie BOCS, Ga\xEBtan DROC" + doi: '' + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - Format validation + - Database search + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Data retrieval + edam_topic: [] + id: b131218bec7eacb4 + latest_version: 4 + license: null + link: https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4 + name: Genfam_introgrice_wf_1.1_prot_build_8_species + number_of_steps: null + source: https://usegalaxy.fr + tags: + - gene + - family + - polypeptide + tools: + - hmm2fasta + - rbc_mafft + - tp_cat + - hmmsearch_db + - hmmer_hmmbuild + - trimal + update_time: '2023-11-22' + versions: 4 +- create_time: '2023-11-22' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + edam_topic: [] + id: 894143d81af8dff0 + latest_version: 3 + license: null + link: https://usegalaxy.fr/published/workflow?id=894143d81af8dff0 + name: Genfam_wf_1.2_prot_phylogeny + number_of_steps: null + source: https://usegalaxy.fr + tags: + - gene + - tree + - protein + tools: + - rbc_mafft + - fastatophylip + - RapGreen + - phyml + - trimal + update_time: '2023-11-22' + versions: 3 +- create_time: '2021-10-07' + creators: + - yguitton + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 32f903738292a67f + latest_version: 9 + license: null + link: https://usegalaxy.fr/published/workflow?id=32f903738292a67f + name: Workflow first steps in 'GCMS' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - metabolomics + - GCMS + - DEMO + - W4M + tools: + - xcms_merge + - Multivariate + - metams_runGC + - abims_xcms_xcmsSet + - msnbase_readmsdata + - xcms_export_samplemetadata + - xcms_plot_chromatogram + update_time: '2023-11-21' + versions: 9 +- create_time: '2020-09-06' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 5ec8a143f82a8c90 + latest_version: 11 + license: null + link: https://usegalaxy.fr/published/workflow?id=5ec8a143f82a8c90 + name: 'LC-HRMS-driven computational toolbox to assess extraction protocols dedicated + to untargeted analysis: How to ease analyzing pesticides-contaminated soils?' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - AnalyticalDevelopment + - LiquidChromatography-HighResolutionMassSpectrometry + - Chemometrics + - SoilMetabolomics + - Pesticides + - UntargetedAnalysis + - UntargetedMetabolicProfiling + tools: + - xcms_merge + - abims_xcms_fillPeaks + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - Batch_correction + update_time: '2023-11-19' + versions: 11 +- create_time: '2023-11-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 0f6714dbdb90b6aa + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=0f6714dbdb90b6aa + name: Workflow v2 + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - collection_column_join + - featurecounts + - hisat2 + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 72b531d980acaa6c + latest_version: 11 + license: null + link: https://usegalaxy.fr/published/workflow?id=72b531d980acaa6c + name: walaa workflow + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - collection_column_join + - featurecounts + - hisat2 + update_time: '2023-11-15' + versions: 11 +- create_time: '2023-11-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 6d2945d35fa956c8 + latest_version: 2 + license: null + link: https://usegalaxy.fr/published/workflow?id=6d2945d35fa956c8 + name: RNAseq + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - collection_column_join + - featurecounts + - hisat2 + update_time: '2023-11-14' + versions: 2 +- create_time: '2023-11-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: e0bad0b97ee71577 + latest_version: 5 + license: null + link: https://usegalaxy.fr/published/workflow?id=e0bad0b97ee71577 + name: RNAseq + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - collection_column_join + - featurecounts + - hisat2 + update_time: '2023-11-14' + versions: 5 +- create_time: '2023-11-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 5e49933a687c2b46 + latest_version: 5 + license: null + link: https://usegalaxy.fr/published/workflow?id=5e49933a687c2b46 + name: Louis Barolle RNAseq analysis + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - collection_column_join + - featurecounts + - hisat2 + update_time: '2023-11-14' + versions: 5 +- create_time: '2023-10-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 74b4d11c07f7f0a4 + latest_version: 0 + license: null + link: https://usegalaxy.fr/published/workflow?id=74b4d11c07f7f0a4 + name: wf_4_m2Immuno + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - bamFilter + - sickle + - wig_to_bigWig + - rseqc_bam2wig + - hisat2 + update_time: '2023-10-20' + versions: 0 +- create_time: '2023-10-12' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + edam_topic: [] + id: e134e9637adfc5b6 + latest_version: 3 + license: null + link: https://usegalaxy.fr/published/workflow?id=e134e9637adfc5b6 + name: genfam_ali_trim_ssb + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - trimal + - rbc_mafft + update_time: '2023-10-12' + versions: 3 +- create_time: '2023-09-19' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + - Nucleic acid sequence analysis + edam_topic: [] + id: e266db902aa1b0e8 + latest_version: 0 + license: null + link: https://usegalaxy.fr/published/workflow?id=e266db902aa1b0e8 + name: RNAseq count one condition + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - rna_star + - htseq_count + update_time: '2023-09-19' + versions: 0 +- create_time: '2023-07-05' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 18b2f77f2915adc7 + latest_version: 4 + license: null + link: https://usegalaxy.fr/published/workflow?id=18b2f77f2915adc7 + name: Mistletoe_LCMS_JPN + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - xcms_merge + - abims_xcms_fillPeaks + - intens_check + - checkFormat + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - Batch_correction + - abims_xcms_xcmsSet + - quality_metrics + update_time: '2023-07-19' + versions: 4 +- create_time: '2022-11-24' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 80c1ec9c609e79ef + latest_version: 5 + license: null + link: https://usegalaxy.fr/published/workflow?id=80c1ec9c609e79ef + name: galaxy 101 24/11 + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2023-05-25' + versions: 5 +- create_time: '2023-03-22' + creators: + - RECETOX + doi: '' + edam_operation: + - Formatting + - Peak detection + - Format validation + - Mass spectrum visualisation + - Chromatogram visualisation + - Standardisation and normalisation + - Validation + - Spectral library search + - Imputation + - Chromatographic alignment + - Clustering + - Filtering + - Correlation + - Label-free quantification + edam_topic: [] + id: 1407c1703f360f07 + latest_version: 1 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=1407c1703f360f07 + name: GC_MS_workflow_using_xcms (imported from URL) + number_of_steps: null + source: https://usegalaxy.fr + tags: + - GC-MS + - Metabolomics + - Expospomics + tools: + - xcms_merge + - abims_xcms_fillPeaks + - riassigner + - matchms + - abims_xcms_retcor + - abims_xcms_group + - metams_runGC + - ramclustr + - cat1 + - abims_xcms_xcmsSet + - msnbase_readmsdata + - msconvert + - matchms_formatter + update_time: '2023-03-24' + versions: 1 +- create_time: '2023-03-23' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 4aa393a1f192a495 + latest_version: 4 + license: null + link: https://usegalaxy.fr/published/workflow?id=4aa393a1f192a495 + name: Anne-claire_metaMS GC WF with RI list + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - xcms_merge + - metams_runGC + - abims_xcms_xcmsSet + - msnbase_readmsdata + - xcms_export_samplemetadata + - xcms_plot_chromatogram + update_time: '2023-03-23' + versions: 4 +- create_time: '2023-03-23' + creators: + - yguitton + doi: '' + edam_operation: + - Validation + - Peak detection + - Chromatographic alignment + - Mass spectrum visualisation + - Filtering + - Chromatogram visualisation + - Label-free quantification + edam_topic: [] + id: cca13353d553319e + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.fr/published/workflow?id=cca13353d553319e + name: short_msPurity_coffee + number_of_steps: null + source: https://usegalaxy.fr + tags: + - lc-msms + - metabolomics + - esi + - positive + - w4m + - dda + - '2023' + tools: + - mspurity_createdatabase + - mspurity_averagefragspectra + - mspurity_frag4feature + - mspurity_filterfragspectra + - abims_xcms_group + - mspurity_spectralmatching + - mspurity_puritya + update_time: '2023-03-23' + versions: 2 +- create_time: '2021-10-26' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 5bfbe77fd6b37c45 + latest_version: 12 + license: null + link: https://usegalaxy.fr/published/workflow?id=5bfbe77fd6b37c45 + name: WF classic positive LC-QTOF + number_of_steps: null + source: https://usegalaxy.fr + tags: + - LC-MS + - QTOF + - ESI+ + - W4M + tools: + - xcms_merge + - abims_xcms_fillPeaks + - intens_check + - checkFormat + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - Multivariate + - Batch_correction + - abims_xcms_xcmsSet + - msnbase_readmsdata + - quality_metrics + - xcms_plot_chromatogram + update_time: '2023-03-22' + versions: 12 +- create_time: '2023-02-11' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Sequence trimming + - DNA barcoding + - Read pre-processing + - Primer removal + edam_topic: [] + id: b5d86d505c09d170 + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=b5d86d505c09d170 + name: Workflow constructed from history 'ASVs Trematodes in Bulinus (Senegal)' + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - dada2_makeSequenceTable + - dada2_seqCounts + - dada2_filterAndTrim + - cutadapt + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2023-02-15' + versions: 1 +- create_time: '2022-04-15' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d0d12c0b80c286f9 + latest_version: 2 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=d0d12c0b80c286f9 + name: 'COVID-19: variation analysis on ARTIC PE data 0.5' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid19.galaxyproject.org + - emergen + - covid-19 + - artic + - latest + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2022-06-08' + versions: 2 +- create_time: '2022-04-15' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 57b5a45c9f71a09c + latest_version: 3 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=57b5a45c9f71a09c + name: 'COVID-19: variation analysis on WGS SE data 0.1.3' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid19.galaxyproject.org + - covid-19 + - emergen + - latest + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2022-04-15' + versions: 3 +- create_time: '2021-08-10' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - SNP detection + - Pairwise sequence alignment + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 727cfdb7c79287d1 + latest_version: 4 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=727cfdb7c79287d1 + name: 'COVID-19: variation analysis of ARTIC ONT data 0.2.1' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - ONT + - covid19.galaxyproject.org + - emergen + - covid-19 + - artic + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - snpeff_sars_cov_2 + - lofreq_filter + - minimap2 + - samtools_view + - tp_find_and_replace + - multiqc + update_time: '2022-04-15' + versions: 4 +- create_time: '2022-04-15' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: b168a179d1b456cb + latest_version: 1 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=b168a179d1b456cb + name: 'COVID-19: variation analysis reporting 0.2' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + - covid19.galaxyproject.org + - emergen + - latest + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-04-15' + versions: 1 +- create_time: '2022-04-15' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: bf8ffe72b7ce4570 + latest_version: 1 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570 + name: 'COVID-19: consensus construction 0.3' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid19.galaxyproject.org + - covid-19 + - emergen + - latest + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-04-15' + versions: 1 +- create_time: '2022-04-15' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 61235264d5d2f666 + latest_version: 1 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=61235264d5d2f666 + name: 'COVID-19: variation analysis of ARTIC ONT data 0.3.1' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + - artic + - ont + - covid19.galaxyproject.org + - emergen + - latest + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2022-04-15' + versions: 1 +- create_time: '2022-04-15' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 54b48eeeed3564dd + latest_version: 1 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=54b48eeeed3564dd + name: 'COVID-19: variation analysis on WGS PE data 0.2.2' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + - covid19.galaxyproject.org + - emergen_validated + - emergen + - latest + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-04-15' + versions: 1 +- create_time: '2022-04-15' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 591c57173e259ca6 + latest_version: 2 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=591c57173e259ca6 + name: 'COVID-19: SARS-CoV-2 Illumina Amplicon pipeline - iVar based 0.2.2' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + - artic + - iwc + - emergen + - latest + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2022-04-15' + versions: 2 +- create_time: '2022-03-14' + creators: + - yguitton + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: bcd348178335a19b + latest_version: 5 + license: CC-BY-4.0 + link: https://usegalaxy.fr/published/workflow?id=bcd348178335a19b + name: Workflow XCMS_CAMERA_msPurity + number_of_steps: null + source: https://usegalaxy.fr + tags: + - LC-MSMS + - Metabolomics + - ESI + - Positive + - W4M + - DDA + tools: + - xcms_merge + - mspurity_createdatabase + - abims_xcms_fillPeaks + - mspurity_averagefragspectra + - mspurity_frag4feature + - mspurity_filterfragspectra + - abims_xcms_group + - mspurity_spectralmatching + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - mspurity_createmsp + - mspurity_puritya + - metfrag + update_time: '2022-03-14' + versions: 5 +- create_time: '2021-12-30' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: e6a55d00f1364794 + latest_version: 2 + license: null + link: https://usegalaxy.fr/published/workflow?id=e6a55d00f1364794 + name: Bordeaux-Global-ESI-pos + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - xcms_merge + - abims_xcms_fillPeaks + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - Batch_correction + - quality_metrics + update_time: '2021-12-30' + versions: 2 +- create_time: '2021-12-22' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: e3d00bdef9addd7c + latest_version: 4 + license: null + link: https://usegalaxy.fr/published/workflow?id=e3d00bdef9addd7c + name: C_Elegans_Publication + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - xcms_merge + - abims_xcms_fillPeaks + - intens_check + - checkFormat + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - Multivariate + - Batch_correction + - abims_xcms_xcmsSet + - msnbase_readmsdata + - abims_xcms_summary + - quality_metrics + - xcms_plot_chromatogram + update_time: '2021-12-22' + versions: 4 +- create_time: '2021-11-02' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: e3c04a30258421aa + latest_version: 2 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=e3c04a30258421aa + name: 'COVID-19: variation analysis of ARTIC ONT data 0.3' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + - artic + - ont + - covid19.galaxyproject.org + - emergen + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2021-11-02' + versions: 2 +- create_time: '2021-09-13' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2345fad7dac13daa + latest_version: 5 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa + name: 'COVID-19: SARS-CoV-2 Illumina Amplicon pipeline - iVar based 0.1' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - emergen + - covid-19 + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2021-09-13' + versions: 5 +- create_time: '2021-09-13' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bffee40c87c7b20a + latest_version: 2 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=bffee40c87c7b20a + name: 'COVID-19: variation analysis on WGS PE data 0.2.1' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid19.galaxyproject.org + - emergen_validated + - emergen + - covid-19 + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2021-09-13' + versions: 2 +- create_time: '2021-09-13' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: ca0bd0e42cb774f9 + latest_version: 2 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=ca0bd0e42cb774f9 + name: 'COVID-19: variation analysis on WGS SE data 0.1.2' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid19.galaxyproject.org + - emergen + - covid-19 + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2021-09-13' + versions: 2 +- create_time: '2021-07-08' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 798c8ff19825ab2c + latest_version: 3 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=798c8ff19825ab2c + name: 'COVID-19: variation analysis reporting 0.1.1' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid19.galaxyproject.org + - emergen + - covid-19 + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2021-09-13' + versions: 3 +- create_time: '2021-08-11' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 98529cff0ef36b91 + latest_version: 2 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=98529cff0ef36b91 + name: 'COVID-19: variation analysis on ARTIC PE data 0.4.1' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid19.galaxyproject.org + - emergen + - covid-19 + - artic + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2021-09-13' + versions: 2 +- create_time: '2021-08-11' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: a3e9062133fdf7c2 + latest_version: 2 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2 + name: 'COVID-19: consensus construction 0.2.1' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid19.galaxyproject.org + - emergen + - covid-19 + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2021-09-13' + versions: 2 +- create_time: '2021-07-17' + creators: [] + doi: '' + edam_operation: + - Variant classification + - Methylation analysis + - Tree-based sequence alignment + - Variant calling + edam_topic: [] + id: feb57548b3ce914d + latest_version: 23 + license: null + link: https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d + name: Full analysis ONT ARTIC + number_of_steps: null + source: https://usegalaxy.fr + tags: + - Emergen-Evaluation + tools: + - pangolin + - nextclade + update_time: '2021-07-18' + versions: 23 +- create_time: '2021-07-17' + creators: [] + doi: '' + edam_operation: + - Variant classification + - Methylation analysis + - Tree-based sequence alignment + - Variant calling + edam_topic: [] + id: e4735d214a68b790 + latest_version: 9 + license: null + link: https://usegalaxy.fr/published/workflow?id=e4735d214a68b790 + name: Full analysis PE Illumina ARTIC + number_of_steps: null + source: https://usegalaxy.fr + tags: + - Emergen-evaluation + tools: + - pangolin + - nextclade + update_time: '2021-07-18' + versions: 9 +- create_time: '2021-06-04' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7d27dd394b921846 + latest_version: 1 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=7d27dd394b921846 + name: 'COVID-19: variation analysis on ARTIC PE data v0.2' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + - emergen + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2021-07-07' + versions: 1 +- create_time: '2021-07-06' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 0df61a88d64de252 + latest_version: 1 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=0df61a88d64de252 + name: 'COVID-19: consensus construction v0.2' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - COVID-19 + - covid19.galaxyproject.org + - emergen + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2021-07-06' + versions: 1 +- create_time: '2021-06-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4665d95259c26985 + latest_version: 5 + license: null + link: https://usegalaxy.fr/published/workflow?id=4665d95259c26985 + name: ARTIC PE variation analysis from nested samples + number_of_steps: null + source: https://usegalaxy.fr + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - __ZIP_COLLECTION__ + - collapse_dataset + update_time: '2021-06-04' + versions: 5 +- create_time: '2021-06-03' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e0b225d4b2556365 + latest_version: 1 + license: MIT + link: https://usegalaxy.fr/published/workflow?id=e0b225d4b2556365 + name: 'COVID-19: variation analysis on ARTIC PE data v0.3' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2021-06-04' + versions: 1 +- create_time: '2020-01-09' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 06fa7dd6eea42350 + latest_version: 4 + license: null + link: https://usegalaxy.fr/published/workflow?id=06fa7dd6eea42350 + name: 'Mass spectrometry: LC-MS analysis (3.4)' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - metabolomics + - gtn + - lcms + tools: + - xcms_merge + - abims_xcms_fillPeaks + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - Univariate + - wsdl_hmdb + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - abims_xcms_summary + - quality_metrics + - Batch_correction + - xcms_plot_chromatogram + update_time: '2021-04-23' + versions: 4 +- create_time: '2020-12-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6babfa7409467035 + latest_version: 4 + license: null + link: https://usegalaxy.fr/published/workflow?id=6babfa7409467035 + name: Workflow_QExactive_DDA_processing_POS + number_of_steps: null + source: https://usegalaxy.fr + tags: + - Metabolomics + - MSMS + - Annotation + - ESI + tools: + - mspurity_createdatabase + - mspurity_averagefragspectra + - mspurity_frag4feature + - mspurity_filterfragspectra + - mspurity_spectralmatching + - mspurity_createmsp + - mspurity_puritya + update_time: '2021-04-06' + versions: 4 +- create_time: '2021-04-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 5d83e0886f2a7465 + latest_version: 2 + license: null + link: https://usegalaxy.fr/published/workflow?id=5d83e0886f2a7465 + name: Workflow constructed from history 'TP omiques' + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + - collection_column_join + - rseqc_read_distribution + - cutadapt + - rseqc_infer_experiment + - multiqc + - picard_MarkDuplicates + - featurecounts + - hisat2 + update_time: '2021-04-04' + versions: 2 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 10073c7392914246 + latest_version: 3 + license: null + link: https://usegalaxy.fr/published/workflow?id=10073c7392914246 + name: "FastQ_St\xE9phanie" + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - fastqc + update_time: '2021-03-19' + versions: 3 +- create_time: '2021-02-25' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 19e99a5c09c01bb7 + latest_version: 2 + license: null + link: https://usegalaxy.fr/published/workflow?id=19e99a5c09c01bb7 + name: Development of an Untargeted Metabolomics Approach for the Impact Evaluation + of Biocontrol Product on Plant Holobiont and Residues Dissipation - W4M Workflow + and Parameters + number_of_steps: null + source: https://usegalaxy.fr + tags: [] + tools: + - xcms_merge + - abims_xcms_fillPeaks + - corrtable + - Analytic_correlation_filtration + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - tp_easyjoin_tool + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - Batch_correction + - quality_metrics + update_time: '2021-02-25' + versions: 2 +- create_time: '2020-09-16' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 2ee479308227a926 + latest_version: 3 + license: null + link: https://usegalaxy.fr/published/workflow?id=2ee479308227a926 + name: 'Electrospray Ionization and heterogeneous matrix effects in Liquid Chromatography-Mass + Spectrometry-based meta-metabolomics: a biomarker or a suppressed ion? - W4M Workflow + and Parameters' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - Biomarkers + - ElectrosprayIonization + - Ionsuppression + - Matrixeffect + - Meta-metabolomics + - LiquidChromatography-MassSpectrometry + tools: + - xcms_merge + - abims_xcms_fillPeaks + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - Batch_correction + - quality_metrics + update_time: '2020-09-24' + versions: 3 +- create_time: '2020-07-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fc89c1db919492da + latest_version: 2 + license: null + link: https://usegalaxy.fr/published/workflow?id=fc89c1db919492da + name: 'Online HS-SPME-GC-MS-based Untargeted Volatile Metabolomics for Studying + Emerging Complex Biopesticides: a Proof of Concept - W4M Workflow and Parameters' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - UntargetedMetabolomics + - Pesticidesofnaturalorigins + - SolidPhaseMicroextraction + - Headspace + - GasChromatography-MassSpectrometry + - ComplexBiopesticides + tools: + - metams_runGC + update_time: '2020-08-27' + versions: 2 +- create_time: '2020-06-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2689019758f56c05 + latest_version: 0 + license: null + link: https://usegalaxy.fr/published/workflow?id=2689019758f56c05 + name: Biomarker_candidate_identification + number_of_steps: null + source: https://usegalaxy.fr + tags: + - proteomics + - proteore + tools: + - IDconverter + - rna_abbased_data + - retrieve_from_hpa + - prot_features + - Jvenn + - tp_cut_tool + - retr_pepatlas1 + - MQoutputfilter + update_time: '2020-06-24' + versions: 0 +- create_time: '2020-06-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3707df4f3f80b034 + latest_version: 0 + license: null + link: https://usegalaxy.fr/published/workflow?id=3707df4f3f80b034 + name: proteome annotation (release 2.1) + number_of_steps: null + source: https://usegalaxy.fr + tags: + - proteomics + - proteore + tools: + - IDconverter + - reactome_analysis + - rna_abbased_data + - retrieve_from_hpa + - Jvenn + - cluter_profiler + - MQoutputfilter + update_time: '2020-06-22' + versions: 0 +- create_time: '2020-06-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 267af6c99eea4fff + latest_version: 0 + license: null + link: https://usegalaxy.fr/published/workflow?id=267af6c99eea4fff + name: Pancreatic_Cancer_Biomarkers_Selection_Strategy_Shared + number_of_steps: null + source: https://usegalaxy.fr + tags: + - proteomics + - proteore + tools: + - sel_ann_hpa + - IDconverter + - retrieve_from_hpa + - prot_features + - Jvenn + - tp_cut_tool + - retr_pepatlas1 + - proteore_get_unique_peptide_srm_method + - MQoutputfilter + update_time: '2020-06-22' + versions: 0 +- create_time: '2020-03-18' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: e96cd8dd62fa0ff8 + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=e96cd8dd62fa0ff8 + name: 'COVID-19: 4- variation analysis PE' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + tools: + - snpSift_extractFields + - collapse_dataset + - lofreq_call + - snpEff_build_gb + - snpEff + - lofreq_viterbi + - samtool_filter2 + - bwa_mem + update_time: '2020-03-25' + versions: 1 +- create_time: '2020-03-18' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Statistical calculation + - Sequence alignment analysis + - Local alignment + - Phylogenetic tree generation (from molecular sequences) + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: 297b71156b297a73 + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=297b71156b297a73 + name: 'COVID-19: 6- Recombination and selection analysis' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + tools: + - hyphy_gard + - rbc_mafft + - 'EMBOSS: tranalign100' + - hyphy_absrel + - fasttree + - 'EMBOSS: transeq101' + update_time: '2020-03-24' + versions: 1 +- create_time: '2020-03-18' + creators: [] + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: b3974acb70608e38 + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=b3974acb70608e38 + name: 'COVID-19: 5- CoV S-gene conservation' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + tools: + - 'EMBOSS: tranalign100' + - 'EMBOSS: transeq101' + - rbc_mafft + update_time: '2020-03-24' + versions: 1 +- create_time: '2020-03-18' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + - Formatting + - Phylogenetic tree generation (from molecular sequences) + edam_topic: [] + id: c7be6e229a045fad + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad + name: 'COVID-19: 3- MRCA analysis' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + tools: + - picard_NormalizeFasta + - Remove beginning1 + - Cut1 + - collapse_dataset + - ncbi_acc_download + - rbc_mafft + - fasttree + - tp_sed_tool + - Convert characters1 + update_time: '2020-03-24' + versions: 1 +- create_time: '2020-03-18' + creators: [] + doi: '' + edam_operation: + - Sequence assembly visualisation + - Aggregation + - Genome assembly + edam_topic: [] + id: 5bb882218afda132 + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=5bb882218afda132 + name: 'COVID-19: 2- assembly of genome sequence' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + tools: + - bandage_image + - spades + - unicycler + - bandage_info + update_time: '2020-03-22' + versions: 1 +- create_time: '2020-03-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Genome indexing + - Sequence composition calculation + - Read mapping + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Generation + - Sequencing quality control + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: 776ef2fa51094ba6 + latest_version: 1 + license: null + link: https://usegalaxy.fr/published/workflow?id=776ef2fa51094ba6 + name: 'COVID-19: 1- read pre-processing with download' + number_of_steps: null + source: https://usegalaxy.fr + tags: + - covid-19 + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - picard_MergeSamFiles + - fasterq_dump + - minimap2 + - multiqc + - samtool_filter2 + - bwa_mem + update_time: '2020-03-22' + versions: 1 +- create_time: '2024-10-17' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: a5241f01bb65bd38 + latest_version: 0 + license: null + link: https://usegalaxy.cz/published/workflow?id=a5241f01bb65bd38 + name: 'GTN Training: Galaxy 101 For Everyone' + number_of_steps: 10 + source: https://usegalaxy.cz + tags: + - introduction + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2024-10-17' + versions: 0 +- create_time: '2024-10-17' + creators: + - Anthony Bretaudeau + doi: '' + edam_operation: + - Fold recognition + - Genome visualisation + - Protein feature detection + - Information extraction + - Genome assembly + - Query and retrieval + - Sequence motif recognition + - Sequence annotation + - Homology-based gene prediction + - Scaffolding + - Genome annotation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 932f4901960a595a + latest_version: 0 + license: GPL-3.0-or-later + link: https://usegalaxy.cz/published/workflow?id=932f4901960a595a + name: Funannotate + number_of_steps: 16 + source: https://usegalaxy.cz + tags: + - genome-annotation + tools: + - aegean_parseval + - funannotate_predict + - eggnog_mapper + - jbrowse + - interproscan + - rna_star + - funannotate_compare + - busco + - funannotate_annotate + update_time: '2024-10-17' + versions: 0 +- create_time: '2024-09-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6acc0e8041609876 + latest_version: 0 + license: null + link: https://usegalaxy.cz/published/workflow?id=6acc0e8041609876 + name: paste_columns + number_of_steps: 3 + source: https://usegalaxy.cz + tags: [] + tools: + - Paste1 + update_time: '2024-09-26' + versions: 0 +- create_time: '2024-09-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e8ddd351204e4f2f + latest_version: 0 + license: null + link: https://usegalaxy.cz/published/workflow?id=e8ddd351204e4f2f + name: paste_columns + number_of_steps: 3 + source: https://usegalaxy.cz + tags: [] + tools: + - Paste1 + update_time: '2024-09-26' + versions: 0 +- create_time: '2024-09-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 526edf41918427e2 + latest_version: 0 + license: null + link: https://usegalaxy.cz/published/workflow?id=526edf41918427e2 + name: paste_columns + number_of_steps: 3 + source: https://usegalaxy.cz + tags: [] + tools: + - Paste1 + update_time: '2024-09-26' + versions: 0 +- create_time: '2024-09-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2b00f1b1ed98268b + latest_version: 0 + license: null + link: https://usegalaxy.cz/published/workflow?id=2b00f1b1ed98268b + name: paste_columns + number_of_steps: 3 + source: https://usegalaxy.cz + tags: [] + tools: + - Paste1 + update_time: '2024-09-26' + versions: 0 +- create_time: '2024-10-19' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 49d3cbacd6112a72 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=49d3cbacd6112a72 + name: Find exons with the highest number of features (imported from URL) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2024-10-19' + versions: 0 +- create_time: '2024-10-18' + creators: [] + doi: '' + edam_operation: + - Formatting + - Data handling + - Taxonomic classification + - Genome alignment + - Mapping + - Query and retrieval + - Data retrieval + - Generation + - Sequence assembly + edam_topic: [] + id: e4dabaf57668dbd1 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 + name: GTDB-TK subworkflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - cami_amber_convert + - gtdb_to_taxdump + - name2taxid + - gtdbtk_classify_wf + - tp_replace_in_column + - compose_text_param + - biobox_add_taxid + - cat_multi_datasets + update_time: '2024-10-18' + versions: 1 +- create_time: '2024-10-18' + creators: [] + doi: '' + edam_operation: + - Genome annotation + - Sequence clustering + - Sequence assembly + - Read mapping + - Read binning + edam_topic: [] + id: 43098b8afe78b071 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=43098b8afe78b071 + name: MAGs taxonomic binning evaluation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - split_file_to_collection + - __RELABEL_FROM_FILE__ + - tp_replace_in_column + - concoct_extract_fasta_bins + - bowtie2 + - concoct_merge_cut_up_clustering + - collection_element_identifiers + - samtools_sort + - concoct + - metabat2_jgi_summarize_bam_contig_depths + - compose_text_param + - semibin + - cami_amber + - cami_amber_add + - tp_awk_tool + - param_value_from_file + - metabat2 + - concoct_coverage_table + - das_tool + - Fasta_to_Contig2Bin + - concoct_cut_up_fasta + - cat_multi_datasets + update_time: '2024-10-18' + versions: 1 +- create_time: '2024-01-26' + creators: + - "Marie Joss\xE9" + doi: '' + edam_operation: [] + edam_topic: [] + id: 4f51080ffe7d57e0 + latest_version: 8 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=4f51080ffe7d57e0 + name: Marine Omics visualisation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Ocean + - Marineomics + - earth-system + tools: + - tp_cut_tool + - obisindicators + - obis_data + update_time: '2024-10-18' + versions: 8 +- create_time: '2024-08-07' + creators: + - "Marie Joss\xE9" + doi: '' + edam_operation: [] + edam_topic: [] + id: 26fe6b0fb6ca2892 + latest_version: 18 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=26fe6b0fb6ca2892 + name: Ocean's variables 2.0 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - earth-system + - Ocean + tools: + - interactive_tool_odv + - interactive_tool_divand + - divand_full_analysis + update_time: '2024-10-17' + versions: 18 +- create_time: '2024-10-17' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Visualisation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 95cb04ffb473623b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=95cb04ffb473623b + name: Workflow constructed from history 'Assembly Level 1' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastq_paired_end_interlacer + - tp_sorted_uniq + - ggplot2_point + - multiqc + update_time: '2024-10-17' + versions: 0 +- create_time: '2024-10-16' + creators: + - Romane Libouban + doi: '' + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Classification + - Annotation + - Sequence annotation + edam_topic: [] + id: 93e576fca98a554d + latest_version: 9 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=93e576fca98a554d + name: lncRNAs annotation workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - feelnc + - cat1 + - gffread + - stringtie + update_time: '2024-10-17' + versions: 9 +- create_time: '2024-06-05' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - Sequence annotation + - Scaffolding + - Sequence analysis + - Transcriptome assembly + - Genome annotation + - RNA-Seq analysis + - Differential protein expression profiling + - Gene prediction + - Editing + - Sequence assembly validation + edam_topic: [] + id: 7de6e20699183cd3 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=7de6e20699183cd3 + name: WF - Demo + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomeannotation + - Helixer + - Visualization + - Red + tools: + - compleasm + - helixer + - gffread + - jcvi_gff_stats + - red + - omark + - jbrowse + - busco + update_time: '2024-10-17' + versions: 4 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: dfb8e0f3c534000e + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e + name: bacterial_genome_annotation (release v1.1.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: a18aed4b03ffd27e + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e + name: bacterial_genome_annotation (release v1.1.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Genome annotation + edam_topic: [] + id: efe6d8a65226505e + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=efe6d8a65226505e + name: BREW3R (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - stringtie + - map_param_value + - stringtie_merge + - brew3r_r + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: 47e14222073e7192 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=47e14222073e7192 + name: Quality and Contamination Control For Genome Assembly (release v1.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fastq + - bacterial-genomics + - taxonomy-assignment + - paired-end + - quality + - ABRomics + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: ebb131f2a6172081 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081 + name: Quality and Contamination Control For Genome Assembly (release v1.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fastq + - bacterial-genomics + - taxonomy-assignment + - paired-end + - quality + - ABRomics + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - abromics-consortium + - ABRomics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: b93333efdab316d8 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=b93333efdab316d8 + name: Bacterial Genome Assembly using Shov (release v1.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: 34df701aa23a9fb3 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3 + name: amr_gene_detection (release v1.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: 1ce523ef51f47134 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134 + name: amr_gene_detection (release v1.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - workflow4metabolomics + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: 2179ba1c33f77f7e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2179ba1c33f77f7e + name: 'Mass spectrometry: GCMS with metaMS (release v0.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metabolomics + - MS + - workflow4metabolomics + - GC-MS + - GTN + - metaMS + tools: + - xcms_merge + - checkFormat + - Multivariate + - metams_runGC + - abims_xcms_xcmsSet + - msnbase_readmsdata + - xcms_plot_chromatogram + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-07-06' + creators: [] + doi: '' + edam_operation: + - Filtering + - Visualisation + - Statistical calculation + - Standardisation and normalisation + edam_topic: [] + id: e1296dbcf34499b0 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=e1296dbcf34499b0 + name: "Determining multivariable association between various meta\u2019omic features\ + \ using MaAslin2" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - maaslin2 + update_time: '2024-10-16' + versions: 2 +- create_time: '2024-10-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4046ff1b3358adbf + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=4046ff1b3358adbf + name: Workflow constructed from history 'My work- 1'_SearchGUI and Peptideshaker + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ident_params + - PeakPickerHiRes + - FileConverter + - cat1 + - peptide_shaker + - dbbuilder + - search_gui + update_time: '2024-10-16' + versions: 0 +- create_time: '2024-10-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 865f470be3c18b08 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=865f470be3c18b08 + name: Workflow constructed from history 'Human Genomics Assignment' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2024-10-13' + versions: 6 +- create_time: '2024-10-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f560e06d23818b4c + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f560e06d23818b4c + name: 'Germline Variant Analysis Workflow ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - CONVERTER_Bam_Bai_0 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2024-10-13' + versions: 1 +- create_time: '2024-10-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ea0524e0b5eab8b9 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=ea0524e0b5eab8b9 + name: 'Workflow NGS Assignment ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2024-10-12' + versions: 1 +- create_time: '2024-10-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3b7c0b64033f38ac + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3b7c0b64033f38ac + name: Emily Byrne GCB1003 assignment + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bwa + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2024-10-11' + versions: 0 +- create_time: '2024-06-24' + creators: [] + doi: '' + edam_operation: + - Sequencing quality control + - Taxonomic classification + - Genome assembly + - De-novo assembly + - Cross-assembly + - Mapping assembly + - Filtering + - Multilocus sequence typing + edam_topic: [] + id: 201e65bcf2b71584 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=201e65bcf2b71584 + name: Porechop-Merge assembly + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - staramr_search + - flye + - fastq_to_fasta_python + - filtlong + - mlst + - kraken2 + - porechop + - kraken-report + update_time: '2024-10-10' + versions: 8 +- create_time: '2024-10-08' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 8b7de28980c455ce + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8b7de28980c455ce + name: Find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - CONVERTER_interval_to_bedstrict_0 + - comp1 + update_time: '2024-10-08' + versions: 1 +- create_time: '2024-10-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c52e8b5ab3e8e958 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=c52e8b5ab3e8e958 + name: Clustering 3k PBMCs with Seurat - Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - table_compute + - seurat_data + - seurat_reduce_dimension + - seurat_create + - csv_to_tabular + - seurat_clustering + - seurat_plot + - seurat_preprocessing + update_time: '2024-10-08' + versions: 2 +- create_time: '2024-10-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d773cbc76253afbf + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=d773cbc76253afbf + name: Cluster 3k PBMCs with Seurat - Workflow - SCTransform Version + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - table_compute + - seurat_data + - seurat_reduce_dimension + - seurat_create + - csv_to_tabular + - seurat_clustering + - seurat_plot + - seurat_preprocessing + update_time: '2024-10-08' + versions: 3 +- create_time: '2024-10-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 26deb6f2521742ea + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=26deb6f2521742ea + name: Cluster 3k PBMCs with Seurat - Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - table_compute + - seurat_data + - seurat_reduce_dimension + - seurat_create + - csv_to_tabular + - seurat_clustering + - seurat_plot + - seurat_preprocessing + update_time: '2024-10-08' + versions: 3 +- create_time: '2024-10-07' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: dc57118a95b10a80 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80 + name: MICRB265 Phylogenetic Tree + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - newick_display + - muscle + - fasttree + update_time: '2024-10-07' + versions: 1 +- create_time: '2024-10-07' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 6588229d0365657f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6588229d0365657f + name: Find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2024-10-07' + versions: 1 +- create_time: '2024-10-01' + creators: + - "B\xE9r\xE9nice Batut" + - Hans-Rudolf Hotz + - Mehmet Tekman + - Pavankumar Videm + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 21315ffd2df2f159 + latest_version: 5 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=21315ffd2df2f159 + name: Clustering 3k PBMC with Scanpy + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:scRNA-seq + - name:single-cell + tools: + - anndata_manipulate + - scanpy_filter + - anndata_inspect + - datamash_ops + - scanpy_cluster_reduce_dimension + - scanpy_normalize + - scanpy_remove_confounders + - scanpy_plot + - anndata_import + - scanpy_inspect + update_time: '2024-10-04' + versions: 5 +- create_time: '2024-08-28' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Structure visualisation + - Genome visualisation + - Pathway visualisation + edam_topic: [] + id: 972db4abc51bb3ab + latest_version: 123 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab + name: TreeValGalAugTwoHaps + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - filter_by_fasta_ids + - Cut1 + - tp_easyjoin_tool + - cat1 + - jbrowse2 + - fasta_compute_length + update_time: '2024-10-04' + versions: 123 +- create_time: '2024-08-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f9a73b39b2051af1 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=f9a73b39b2051af1 + name: TreeValGalMashmaps2haps + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mashmap + update_time: '2024-10-04' + versions: 3 +- create_time: '2024-06-19' + creators: + - Timon Schlegel + doi: '' + edam_operation: [] + edam_topic: [] + id: d20fbb95f15386f5 + latest_version: 30 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=d20fbb95f15386f5 + name: Multisample Batch Correction with SnapATAC2 and Harmony + number_of_steps: null + source: https://usegalaxy.eu + tags: + - epigenetics + - scATAC-seq + - name:single-cell + tools: + - anndata_manipulate + - collection_element_identifiers + - snapatac2_preprocessing + - __EXTRACT_DATASET__ + - snapatac2_plotting + - __FILTER_FROM_FILE__ + - snapatac2_clustering + - Show beginning1 + update_time: '2024-10-03' + versions: 30 +- create_time: '2024-10-03' + creators: + - GalaxyP + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: 0135ee4b3fa0cbce + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=0135ee4b3fa0cbce + name: Clinical Metaproteomics Quantitation (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:clinicalMP + tools: + - Grouping1 + - Grep1 + - maxquant + - Cut1 + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 70ec8b1719e25982 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=70ec8b1719e25982 + name: 'COVID-19: variation analysis reporting (release v0.3.4)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 52bdf400f97c5770 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=52bdf400f97c5770 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.5.3)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-08-17' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Sequence analysis + - Genome visualisation + - Pathway visualisation + - Structural variation detection + edam_topic: [] + id: df08e520ec3dbcb7 + latest_version: 201 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7 + name: dimer density SV and coverage + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sniffles + - Cut1 + - filter_by_fasta_ids + - tp_replace_in_line + - Add_a_column1 + - deeptools_bam_compare + - tp_easyjoin_tool + - cat1 + - deeptools_bigwig_compare + - jbrowse2 + - minimap2 + - samtools_view + - deeptools_bam_coverage + - pick_value + - fasta_compute_length + update_time: '2024-10-02' + versions: 201 +- create_time: '2024-02-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 21363a774a7575f0 + latest_version: 18 + license: null + link: https://usegalaxy.eu/published/workflow?id=21363a774a7575f0 + name: OSPD example algal workflow - map plot + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Chlorophyll-a + - OSPD + tools: + - c3s + - psy_maps + update_time: '2024-10-02' + versions: 18 +- create_time: '2024-08-28' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Pairwise sequence alignment + - Sequence analysis + - Genome annotation + - Data handling + - Mapping + - Structural variation detection + - Sequence file editing + edam_topic: [] + id: 2880a32a52d27743 + latest_version: 41 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2880a32a52d27743 + name: TreeValGalBaseOneHaplotype + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sniffles + - seqtk_telo + - bedtools_makewindowsbed + - bbgtobigwig + - windowmasker_mkcounts + - Add_a_column1 + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - minimap2 + - deeptools_bam_coverage + - pick_value + - fasta_compute_length + update_time: '2024-10-02' + versions: 41 +- create_time: '2024-09-30' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: f21d6a40a10a8ae8 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8 + name: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + tools: + - mothur_heatmap_sim + - mothur_make_biom + - mothur_cluster + - mothur_rarefaction_single + - mothur_align_seqs + - mothur_classify_seqs + - mothur_venn + - taxonomy_krona_chart + - mothur_get_groups + - mothur_seq_error + - mothur_make_shared + - newick_display + - mothur_remove_groups + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_dist_shared + - mothur_dist_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_tree_shared + - mothur_unique_seqs + - mothur_classify_otu + - mothur_taxonomy_to_krona + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - XY_Plot_1 + - mothur_count_groups + - mothur_cluster_split + - mothur_sub_sample + - mothur_pre_cluster + update_time: '2024-10-01' + versions: 1 +- create_time: '2024-08-06' + creators: + - Bryan Wee + - Marianne Keith + doi: '' + edam_operation: + - Statistical calculation + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Box-Whisker plot plotting + - Sequence assembly + - Sequence assembly visualisation + - Filtering + - Sequence assembly validation + - Sequencing quality control + - Parsing + - Data handling + - Base-calling + - Genome assembly + - Sequence composition calculation + - Multilocus sequence typing + - Visualisation + - Cross-assembly + - Mapping assembly + - Scatter plot plotting + edam_topic: [] + id: eb5ab8bc82569eee + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee + name: Nanopore AMR Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - nanoplot + - medaka_consensus_pipeline + - quast + - abricate + - bandage_info + - flye + - staramr_search + - hamronize_tool + - hamronize_summarize + - filtlong + - mlst + - abritamr + - ncbi_blastn_wrapper + - bandage_image + - amrfinderplus + update_time: '2024-10-01' + versions: 13 +- create_time: '2024-09-12' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Formatting + - Taxonomic classification + - Data handling + - Sequence file editing + - Demultiplexing + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 8f747dbff3216993 + latest_version: 23 + license: null + link: https://usegalaxy.eu/published/workflow?id=8f747dbff3216993 + name: aioA amplicon analysis with "Double" Chimera remove process + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_text_file_with_recurring_lines + - qiime_pick_otus + - qiime_make_otu_table + - ncbi_tblastx_wrapper + - blastxml_to_top_descr + - mothur_remove_seqs + - mothur_chimera_vsearch + - ncbi_blastx_wrapper + - blastxml_to_tabular + - mothur_screen_seqs + - mothur_make_contigs + - cshl_fastx_trimmer + - qiime_pick_rep_set + - biom_summarize_table + - seqtk_sample + - biopython_base_distribution + update_time: '2024-10-01' + versions: 23 +- create_time: '2024-09-06' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Formatting + - Taxonomic classification + - Data handling + - Sequence file editing + - Demultiplexing + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: e14b81a8c0b1b7a4 + latest_version: 52 + license: null + link: https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4 + name: aioA amplicon analysis with "Single" Chimera remove process + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_text_file_with_recurring_lines + - qiime_pick_otus + - qiime_make_otu_table + - ncbi_tblastx_wrapper + - blastxml_to_top_descr + - ncbi_blastx_wrapper + - blastxml_to_tabular + - mothur_screen_seqs + - mothur_make_contigs + - cshl_fastx_trimmer + - qiime_pick_rep_set + - biom_summarize_table + - seqtk_sample + - biopython_base_distribution + update_time: '2024-10-01' + versions: 52 +- create_time: '2024-05-22' + creators: + - Rand Zoabi + doi: '' + edam_operation: [] + edam_topic: [] + id: 05dc8f4321a42cdc + latest_version: 68 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=05dc8f4321a42cdc + name: MGnify amplicon summary tables + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MGnify_Amplicon + - amplicon + - metagenomics + tools: + - collection_column_join + - filter_tabular + - query_tabular + - Grouping1 + - tp_awk_tool + update_time: '2024-09-27' + versions: 68 +- create_time: '2024-09-24' + creators: [] + doi: '' + edam_operation: + - Expression analysis + - Rarefaction + - Phylogenetic reconstruction + - Pathway analysis + edam_topic: [] + id: be9ff4159593cc34 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34 + name: history 'qiime2 hackathon' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - picrust2_pipeline + - qiime_extract_viz + - qiime2__feature_classifier__classify_sklearn + - qiime2__demux__summarize + - qiime2_core__tools__import + - qiime2_core__tools__export + - qiime2__taxa__collapse + - qiime2__feature_table__relative_frequency + - qiime2__dada2__denoise_paired + update_time: '2024-09-26' + versions: 8 +- create_time: '2024-05-17' + creators: + - Rand Zoabi + - Mara Besemer + doi: '' + edam_operation: + - Analysis + - Visualisation + edam_topic: [] + id: 478c921b4914169c + latest_version: 28 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=478c921b4914169c + name: MAPseq to ampvis2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - collection_column_join + - collapse_dataset + - query_tabular + - ampvis2_load + - tp_awk_tool + update_time: '2024-09-26' + versions: 28 +- create_time: '2024-08-21' + creators: + - Marie Lefebvre + doi: '' + edam_operation: + - Visualisation + - Sequence clustering + - Sequence cluster visualisation + - Sequence annotation + edam_topic: [] + id: 86465932556bc96c + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=86465932556bc96c + name: virannot_post_CLC + number_of_steps: null + source: https://usegalaxy.eu + tags: + - virology + - otu + - virannot + - RPS + - virus + tools: + - ncbi_rpstblastn_wrapper + - taxonomy_krona_chart + - ncbi_tblastx_wrapper + - krona-text + - virannot_blast2tsv + - virannot_otu + - virAnnot_rps2tsv + update_time: '2024-09-26' + versions: 6 +- create_time: '2024-09-26' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: d8db0b2e30370b84 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84 + name: bacterial_genome_annotation (release v1.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - abromics-consortium + - ABRomics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 723e718f37e9ab91 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91 + name: Bacterial Genome Assembly using Shov (release v1.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: e37cc0b64774561b + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b + name: amr_gene_detection (release v1.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: a3cb75fd31ba0689 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a3cb75fd31ba0689 + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: c4327bccfa623f7e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c4327bccfa623f7e + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: c4fc3adf8f7ff2bc + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.eu/published/workflow?id=c4fc3adf8f7ff2bc + name: Assembly-decontamination-VGP9 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 2497292e98937a5f + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.eu/published/workflow?id=2497292e98937a5f + name: Assembly-decontamination-VGP9 (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + - Filter1 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 2c2f0b4312bae4f4 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.eu/published/workflow?id=2c2f0b4312bae4f4 + name: Assembly-decontamination-VGP9 (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - ncbi_blastn_wrapper + - parse_mito_blast + - Filter1 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 020f877513f2d0d1 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=020f877513f2d0d1 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 117177b0c231dc55 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=117177b0c231dc55 + name: Get Confident Peaks From ChIP_PE replicates (release v1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 0ae360bfbb3b2494 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0ae360bfbb3b2494 + name: Get Confident Peaks From ChIP_SR replicates (release v1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: d6809603f46de1b3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d6809603f46de1b3 + name: RNAseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 409336bf210033a2 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=409336bf210033a2 + name: RNAseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a76629eccfdeafb8 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a76629eccfdeafb8 + name: ChIPseq_SR (release v0.12) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 30e7dc81e323cbdb + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=30e7dc81e323cbdb + name: ATACseq (release v0.17) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b5e3360f933d1950 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b5e3360f933d1950 + name: ChIPseq_PE (release v0.12) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 478190607a114390 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=478190607a114390 + name: CUTandRUN (release v0.13) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6173008772bdba09 + latest_version: 10 + license: null + link: https://usegalaxy.eu/published/workflow?id=6173008772bdba09 + name: Workflow constructed from history 'Crim OGC API Processes workflow' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Show beginning1 + - hirondelle_crim + update_time: '2024-09-25' + versions: 10 +- create_time: '2024-08-11' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + - Phylogenetic inference + - Phylogenetic tree visualisation + - Visualisation + - Conversion + - Phylogenetic tree analysis + - Nucleic acid sequence analysis + - Phylogenetic tree editing + edam_topic: [] + id: 79b4ae4403772098 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=79b4ae4403772098 + name: Microbiome workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - taxonomy_krona_chart + - Cut1 + - export2graphlan + - graphlan + - graphlan_annotate + - metaphlan + update_time: '2024-09-23' + versions: 0 +- create_time: '2023-06-29' + creators: [] + doi: '' + edam_operation: + - Sequence alignment analysis + - Read mapping + - Coding region prediction + - Aggregation + - Genome annotation + - Sequence assembly + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + - Taxonomic classification + - Data handling + - Genome assembly + - Genome indexing + - Optimisation and refinement + - Sequence contamination filtering + - Visualisation + - Gene prediction + - Generation + - Sequence alignment + edam_topic: [] + id: 98bfad0c684011e9 + latest_version: 56 + license: null + link: https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9 + name: De novo assembly pipeline for viral sequences + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Illumina + - denovo + - RNASeq + - DNASeq + tools: + - __UNZIP_COLLECTION__ + - collapse_dataset + - spades + - bamtools_split_ref + - kraken2 + - fastp + - tp_cat + - regex_replace + - prokka + - qualimap_bamqc + - velvetoptimiser + - megahit + - bwa_mem + - samtools_fastx + - krakentools_extract_kraken_reads + - fasta_filter_by_length + - quast + - samtools_view + - cap3 + - ivar_consensus + - bandage_image + update_time: '2024-09-23' + versions: 56 +- create_time: '2024-08-17' + creators: + - Ross Lazarus + doi: '' + edam_operation: [] + edam_topic: [] + id: 3b94f511c52da835 + latest_version: 36 + license: null + link: https://usegalaxy.eu/published/workflow?id=3b94f511c52da835 + name: dimer density one hap subworkflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - pick_value + - microsatbed + - bigwig_outlier_bed + update_time: '2024-09-22' + versions: 36 +- create_time: '2024-09-20' + creators: + - Wendi Bacon + - The Open University + - Julia Jakiela + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: e2391c40d24d403f + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f + name: LOCKED | Import and Analyse from EBI - Universal - NO MITO + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + - name:training + - name:public-data + tools: + - scanpy_read_10x + - scanpy_compute_graph + - scanpy_normalise_data + - join1 + - scanpy_filter_cells + - scanpy_find_variable_genes + - retrieve_scxa + - scanpy_scale_data + - scanpy_find_markers + - tp_grep_tool + - scanpy_run_pca + - anndata_inspect + - regexColumn1 + - scanpy_run_tsne + - scanpy_run_umap + - anndata_ops + - datamash_transpose + - scanpy_find_cluster + - scanpy_plot_embed + - scanpy_filter_genes + - scanpy_plot + update_time: '2024-09-20' + versions: 2 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: a91c46b9e0c1d635 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635 + name: 'QIIME2 VI: Diversity metrics and estimations (release v0.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - qiime2_core__tools__import + - qiime2__diversity__core_metrics_phylogenetic + - __BUILD_LIST__ + - qiime2__diversity__beta_group_significance + - qiime2__diversity__alpha_group_significance + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 803277b4b0041f94 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=803277b4b0041f94 + name: QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: [] + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: ad8b6d73c9654305 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305 + name: Taxonomy Profiling and Visualization with Kron (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - kraken2 + - krakentools_kreport2krona + - taxonomy_krona_chart + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Visualisation + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Mapping + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: f6a763951d815944 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=f6a763951d815944 + name: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release + v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - collection_column_join + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - ggplot2_heatmap + - fasta2tab + - tp_replace_in_column + - tp_sorted_uniq + - clustalw + - Remove beginning1 + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - tp_split_on_column + - newick_display + - Count1 + - regexColumn1 + - bedtools_getfastabed + - tp_multijoin_tool + - Cut1 + - fasttree + - tab2fasta + - __FILTER_EMPTY_DATASETS__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - "B\xE9r\xE9nice Batut" + - Engy Nasr + - Paul Zierep + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Visualisation + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: 344cd3a3c2ce5302 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302 + name: Nanopore Preprocessing (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:Nanopore + - name:IWC + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - krakentools_extract_kraken_reads + - collection_column_join + - Cut1 + - collapse_dataset + - Add_a_column1 + - __FILTER_FAILED_DATASETS__ + - bamtools_split_mapped + - regexColumn1 + - kraken2 + - porechop + - Grep1 + - minimap2 + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + edam_topic: [] + id: 77e5bbd317750915 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=77e5bbd317750915 + name: Gene-based Pathogen Identification (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:PathoGFAIR + - name:IWC + - name:microGalaxy + tools: + - abricate + - medaka_consensus_pipeline + - collection_element_identifiers + - split_file_to_collection + - flye + - fasta2tab + - bandage_image + - tab2fasta + - compose_text_param + - tp_find_and_replace + - __BUILD_LIST__ + - param_value_from_file + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Variant calling + - Pairwise sequence alignment + edam_topic: [] + id: d215a2e554fd83bc + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc + name: Allele-based Pathogen Identification (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - clair3 + - CONVERTER_gz_to_uncompressed + - table_compute + - snpSift_filter + - Count1 + - Remove beginning1 + - Cut1 + - snpSift_extractFields + - collapse_dataset + - samtools_coverage + - regexColumn1 + - tp_cut_tool + - bcftools_norm + - tp_head_tool + - samtools_depth + - Paste1 + - minimap2 + - bcftools_consensus + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Variant calling + - Pairwise sequence alignment + edam_topic: [] + id: cdf2f02428f5f83f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f + name: Allele-based Pathogen Identification (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - clair3 + - CONVERTER_gz_to_uncompressed + - table_compute + - snpSift_filter + - Count1 + - Remove beginning1 + - Cut1 + - snpSift_extractFields + - collapse_dataset + - samtools_coverage + - regexColumn1 + - tp_cut_tool + - bcftools_norm + - tp_head_tool + - samtools_depth + - Paste1 + - minimap2 + - bcftools_consensus + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 389d992ff7268247 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=389d992ff7268247 + name: Generate Nx and Size plots for multiple assemblies (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - addName + - collapse_dataset + - Add_a_column1 + - Cut1 + - datamash_ops + - gfastats + - param_value_from_file + - tp_awk_tool + - compose_text_param + - ggplot2_point + - addValue + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 9aa290ce1927d700 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=9aa290ce1927d700 + name: Generate Nx and Size plots for multiple assemblies (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - addName + - collapse_dataset + - Add_a_column1 + - Cut1 + - datamash_ops + - gfastats + - param_value_from_file + - tp_awk_tool + - compose_text_param + - ggplot2_point + - addValue + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: 61948fcaefa1418a + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a + name: bacterial_genome_annotation (release v1.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: 8792eaecb69fbc26 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26 + name: bacterial_genome_annotation (release v1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: 36ea584e0f60893e + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e + name: bacterial_genome_annotation (release v1.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: bcd50e655809cfcb + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb + name: bacterial_genome_annotation (release v1.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: 4a218fb93d78ba67 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67 + name: bacterial_genome_annotation (release v1.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Genome annotation + edam_topic: [] + id: a6d36048d545bca7 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=a6d36048d545bca7 + name: BREW3R (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - stringtie + - map_param_value + - stringtie_merge + - brew3r_r + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: 884a4415b669690c + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=884a4415b669690c + name: Quality and Contamination Control For Genome Assembly (release v1.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fastq + - bacterial-genomics + - taxonomy-assignment + - paired-end + - quality + - ABRomics + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: aafcfcb585c5ca75 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75 + name: Quality and Contamination Control For Genome Assembly (release v1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fastq + - bacterial-genomics + - taxonomy-assignment + - paired-end + - quality + - ABRomics + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: 0c47571d20535426 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=0c47571d20535426 + name: Quality and Contamination Control For Genome Assembly (release v1.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fastq + - bacterial-genomics + - taxonomy-assignment + - paired-end + - quality + - ABRomics + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: 0a82eb8b44d9d502 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502 + name: Quality and Contamination Control For Genome Assembly (release v1.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomics + - fastq + - bacterial-genomics + - taxonomy-assignment + - paired-end + - quality + - ABRomics + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - abromics-consortium + - Abromics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 3d937648809ca4e7 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7 + name: Bacterial Genome Assembly using Shov (release v1.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - abromics-consortium + - ABRomics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: fca458178b3c794a + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=fca458178b3c794a + name: Bacterial Genome Assembly using Shov (release v1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - abromics-consortium + - ABRomics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 4216424f032c055f + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=4216424f032c055f + name: Bacterial Genome Assembly using Shov (release v1.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: 41d207d06a32ba05 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05 + name: amr_gene_detection (release v1.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: abe85758e77c78e6 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6 + name: amr_gene_detection (release v1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: f30f8e7dcd50cd0d + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d + name: amr_gene_detection (release v1.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: e1f08a63fbc8e173 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173 + name: 'QIIME2 IIb: Denoising (sequence quality control) and feature table creation + (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - qiime2__feature_table__summarize + - qiime2__feature_table__tabulate_seqs + - qiime2__metadata__tabulate + - qiime2__dada2__denoise_paired + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 5223c9554718114d + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5223c9554718114d + name: 'QIIME2 IIa: Denoising (sequence quality control) and feature table creation + (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - qiime2__feature_table__summarize + - qiime2__dada2__denoise_single + - qiime2__feature_table__tabulate_seqs + - qiime2__metadata__tabulate + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: b2975bb705d3e851 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851 + name: 'QIIME2 Id: Demultiplexed data (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - collection_element_identifiers + - qiime2__demux__summarize + - qiime2_core__tools__import + - __RELABEL_FROM_FILE__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: c58941443cec9380 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c58941443cec9380 + name: 'QIIME2 Ic: Demultiplexed data (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - collection_element_identifiers + - qiime2__demux__summarize + - qiime2_core__tools__import + - __RELABEL_FROM_FILE__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: fb96000c99db2fa8 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8 + name: 'QIIME2 Ib: multiplexed data (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - qiime2__demux__emp_paired + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: c0b5b499b149005f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f + name: 'QIIME2 Ia: multiplexed data (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - qiime2__demux__emp_single + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Matthias Bernt + - UFZ Leipzig + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: 642f4c47028031d7 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=642f4c47028031d7 + name: dada2 amplicon analysis pipeline - for paired en (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:amplicon + tools: + - dada2_makeSequenceTable + - __UNZIP_COLLECTION__ + - dada2_seqCounts + - dada2_assignTaxonomyAddspecies + - dada2_filterAndTrim + - __APPLY_RULES__ + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 5bf6718e7d6158d2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=5bf6718e7d6158d2 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 032a7281a86eba0d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=032a7281a86eba0d + name: Purging-duplicates-one-haplotype-VGP6b (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: d02458f1d7d9c3f4 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=d02458f1d7d9c3f4 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_grep_tool + - tp_cut_tool + - tp_awk_tool + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: aef62f4d0bba003b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=aef62f4d0bba003b + name: Purging-duplicates-one-haplotype-VGP6b (release v0.7.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_grep_tool + - tp_cut_tool + - tp_awk_tool + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-03-31' + creators: + - Ross Lazarus + - Anna Syme + - Delphine Lariviere + - Nadolina Brajuka + doi: '' + edam_operation: + - Pairwise sequence alignment + - Mapping + - Sequence alignment + - Protein sequence analysis + edam_topic: [] + id: 0c92c3c322c3effe + latest_version: 36 + license: null + link: https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe + name: TreeValGal_anno_bed_optional + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + - miniprot + - pick_value + - bedtools_bamtobed + update_time: '2024-09-19' + versions: 36 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fb015e398373ea8a + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=fb015e398373ea8a + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.9) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: b4948afacccfefdb + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=b4948afacccfefdb + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.10) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 847403b72dd346ff + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=847403b72dd346ff + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.11) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 3a3e2d50fe7a9ee3 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=3a3e2d50fe7a9ee3 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 4856e3522b2ee059 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=4856e3522b2ee059 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 3eb6663a66f8e69a + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=3eb6663a66f8e69a + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: f1ca4289ee4f67bb + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=f1ca4289ee4f67bb + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: e8f9e1d911683b22 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=e8f9e1d911683b22 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 1ac0a15758277730 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=1ac0a15758277730 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: c508c00e81018dd8 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=c508c00e81018dd8 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: e7aebe58411d97ed + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=e7aebe58411d97ed + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 319bc351f7a8e358 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=319bc351f7a8e358 + name: Scaffolding-BioNano-VGP7 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: f6bd10486a0ba17d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=f6bd10486a0ba17d + name: Scaffolding-BioNano-VGP7 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - tp_find_and_replace + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: dec16871152fac35 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=dec16871152fac35 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 0e642b5407dd595b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=0e642b5407dd595b + name: kmer-profiling-hifi-VGP1 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 29b4710cd24995b2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=29b4710cd24995b2 + name: kmer-profiling-hifi-VGP1 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: b5de94e9cde071ab + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=b5de94e9cde071ab + name: Purge-duplicate-contigs-VGP6 (release v0.3.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 6c14b08a7ef7e79a + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=6c14b08a7ef7e79a + name: Purge-duplicate-contigs-VGP6 (release v0.3.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 0a3ebee985c26060 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=0a3ebee985c26060 + name: Purge-duplicate-contigs-VGP6 (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_cut_tool + - cat1 + - tp_awk_tool + - compose_text_param + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: feeb1fa358ccf328 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=feeb1fa358ccf328 + name: Scaffolding-HiC-VGP8 (release v0.2.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 0c3ce9feb83f7920 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920 + name: Scaffolding-HiC-VGP8 (release v0.2.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 652433160b04b232 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=652433160b04b232 + name: Scaffolding-HiC-VGP8 (release v0.2.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 31f8c7c46207432f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f + name: Scaffolding-HiC-VGP8 (release v0.2.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 4949751217c0e211 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=4949751217c0e211 + name: Scaffolding-HiC-VGP8 (release v0.2.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 3b57fc81001667b5 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5 + name: Scaffolding with Hi-C data VGP8 (release v0.2.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - compose_text_param + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 7341ca7572447d60 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7341ca7572447d60 + name: baredSC_2d_logN (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 49d913cefc5daaf3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=49d913cefc5daaf3 + name: baredSC_1d_logN (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 023a0ee62dd1f593 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=023a0ee62dd1f593 + name: Assembly-Hifi-only-VGP3 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: e935d2c8ffb52588 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=e935d2c8ffb52588 + name: Assembly-Hifi-only-VGP3 (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: bef0a7d604f2ebef + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=bef0a7d604f2ebef + name: Assembly-Hifi-only-VGP3 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 57cc33ed64d71982 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=57cc33ed64d71982 + name: Assembly-Hifi-only-VGP3 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: b8baade87e733fce + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=b8baade87e733fce + name: Assembly-Hifi-only-VGP3 (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 089e5e83b1de0511 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=089e5e83b1de0511 + name: Assembly-Hifi-only-VGP3 (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: bcf99cc0469db276 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=bcf99cc0469db276 + name: Assembly-Hifi-only-VGP3 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Matthias Bernt + doi: '' + edam_operation: [] + edam_topic: [] + id: da10c475c83c5469 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=da10c475c83c5469 + name: MetaProSIP OpenMS 2.8 (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - FalseDiscoveryRate + - FeatureFinderMultiplex + - IDMapper + - MSGFPlusAdapter + - DecoyDatabase + - MetaProSIP + - __SORTLIST__ + - PeptideIndexer + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 2f094f5e1f391529 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2f094f5e1f391529 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: a639ea0419de1078 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a639ea0419de1078 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 5cc732a6b4338bf5 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5cc732a6b4338bf5 + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 079e2a968d8e6176 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=079e2a968d8e6176 + name: Get Confident Peaks From ChIP_PE replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 1c267e93aa8015e6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1c267e93aa8015e6 + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: b57c3522bdd7c2d5 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b57c3522bdd7c2d5 + name: Get Confident Peaks From ChIP_SR replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Viktoria Isabel Schwarz + - Wolfgang Maier + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Genome indexing + - Read mapping + - Global alignment + - Validation + - Sequence contamination filtering + - Sequence analysis + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6e1fe7372e93fae0 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0 + name: Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - pox + - virology + tools: + - 'EMBOSS: maskseq51' + - split_file_to_collection + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - fasta_compute_length + - collection_element_identifiers + - datamash_ops + - Grep1 + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - samtools_merge + - tp_cat + - tp_sed_tool + - __SORTLIST__ + - qualimap_bamqc + - __APPLY_RULES__ + - param_value_from_file + - bwa_mem + - Cut1 + - __ZIP_COLLECTION__ + - ivar_consensus + - samtools_view + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: d9fc0df2a159e542 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d9fc0df2a159e542 + name: Hi-C_juicermediumtabixToCool_c (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_balance + - cooler_makebins + - cooler_cload_tabix + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 4464d3b0fc782a1a + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4464d3b0fc782a1a + name: cHi-C_fastqToCool_hicup_c (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + - compose_text_param + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 9843ae66c3b367b7 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9843ae66c3b367b7 + name: Hi-C_fastqToCool_hicup_c (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: ead0f264798f9418 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ead0f264798f9418 + name: RNAseq_PE (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 9da26c5131603b9f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9da26c5131603b9f + name: RNAseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: c4fa05e209a2f082 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c4fa05e209a2f082 + name: RNAseq_SR (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 0eb137cd936bbfe0 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0eb137cd936bbfe0 + name: RNAseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b84fd6a0e2632ad9 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b84fd6a0e2632ad9 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: de9003e589631029 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=de9003e589631029 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 326d4102190b74fc + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=326d4102190b74fc + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 94b9287365ea4d0d + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=94b9287365ea4d0d + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2f51a82838722bec + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2f51a82838722bec + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c9aff55e39e195e3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c9aff55e39e195e3 + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 77d2adf5249eb826 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=77d2adf5249eb826 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 503a2f4caacaf63e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=503a2f4caacaf63e + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 4176b9d43325a8d8 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4176b9d43325a8d8 + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2c5cae1389c11881 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2c5cae1389c11881 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 830eb4faff21eb0c + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=830eb4faff21eb0c + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9c24df68dc7d25a4 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9c24df68dc7d25a4 + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 526a93b9f6dfe5ce + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=526a93b9f6dfe5ce + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: ebb51874b533738e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ebb51874b533738e + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-07-12' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Statistical calculation + - Variant calling + edam_topic: [] + id: c879060c00aab94f + latest_version: 10 + license: null + link: https://usegalaxy.eu/published/workflow?id=c879060c00aab94f + name: Nanopore IR KDR - VEP Analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + - freebayes + update_time: '2024-09-16' + versions: 10 +- create_time: '2024-09-16' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: e3165c295bc243e4 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e3165c295bc243e4 + name: Find exons with the highest number of features_CatM + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - CONVERTER_interval_to_bedstrict_0 + - comp1 + update_time: '2024-09-16' + versions: 1 +- create_time: '2024-09-16' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 6c0560c041bde8c6 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=6c0560c041bde8c6 + name: Find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - CONVERTER_interval_to_bedstrict_0 + - comp1 + update_time: '2024-09-16' + versions: 2 +- create_time: '2024-09-11' + creators: + - Michele Bortolomeazzi + doi: '' + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: 7d7550ce7004d71e + latest_version: 19 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e + name: Nuclei Segmentation Example + number_of_steps: null + source: https://usegalaxy.eu + tags: + - imageanaylsis + tools: + - idr_download_by_ids + - ip_threshold + - __EXTRACT_DATASET__ + - ip_overlay_images + - ip_binary_to_labelimage + - ip_filter_standard + - ip_histogram_equalization + update_time: '2024-09-13' + versions: 19 +- create_time: '2024-08-16' + creators: + - Menna + doi: '' + edam_operation: + - Gene-set enrichment analysis + edam_topic: [] + id: 5f053303601cc630 + latest_version: 40 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5f053303601cc630 + name: GO Enrichment Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - goenrichment + - gprofiler_gost + - Cut1 + - tp_split_on_column + update_time: '2024-09-10' + versions: 40 +- create_time: '2024-09-08' + creators: + - "B\xE9r\xE9nice Batut" + - "Teresa M\xFCller" + - Polina Polunina + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Sequence contamination filtering + - Visualisation + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: 181e751be8dd9abc + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc + name: "L\u0160MB: Identification of the micro-organisms in a beer using Nanopore\ + \ sequencing" + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Microbiome + tools: + - fastqc + - nanoplot + - fastp + - taxonomy_krona_chart + - krakentools_kreport2krona + - kraken2 + - porechop + - Filter1 + update_time: '2024-09-08' + versions: 0 +- create_time: '2024-09-08' + creators: + - RECETOX + doi: '' + edam_operation: + - Peak detection + - Format validation + - Alignment + - Standardisation and normalisation + - Spectral library search + - Imputation + - Chromatographic alignment + - Clustering + - Quantification + - Feature extraction + - Filtering + - Correlation + edam_topic: [] + id: 3086366b744e8da9 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3086366b744e8da9 + name: GC-EI-HRMS Annotation Workflow (imported from URL) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Exposomics + - GC-MS + - Metabolomics + - LC-ESI-MS2viaDIA + tools: + - riassigner + - matchms_metadata_match + - recetox_aplcms_generate_feature_table + - waveica + - recetox_aplcms_compute_template + - matchms_spectral_similarity + - recetox_aplcms_align_features + - recetox_aplcms_compute_clusters + - recetox_aplcms_correct_time + - recetox_aplcms_recover_weaker_signals + - ramclustr + - rename_annotated_feature + - recetox_aplcms_remove_noise + - matchms_formatter + update_time: '2024-09-08' + versions: 0 +- create_time: '2024-09-05' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Gene-set enrichment analysis + edam_topic: [] + id: e04be1ab5a16eb9f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f + name: Persist-seq Pseudo-bulk EdgeR v0.4.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fgsea + - collection_element_identifiers + - split_file_to_collection + - tp_replace_in_line + - column_remove_by_header + - query_tabular + - tp_replace_in_column + - oncoenrichr_wrapper + - volcanoplot + - edger + - decoupler_pseudobulk + - param_value_from_file + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-03' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 5cb54278075696ca + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=5cb54278075696ca + name: Galaxy Hi C with updated BWA-MEM + number_of_steps: null + source: https://usegalaxy.eu + tags: + - epigenetics + tools: + - hicexplorer_hicmergematrixbins + - hicexplorer_hiccorrectmatrix + - hicexplorer_hicplotmatrix + - hicexplorer_hicplottads + - hicexplorer_hicbuildmatrix + - hicexplorer_hicfindtads + - hicexplorer_hicpca + - bwa_mem + update_time: '2024-09-03' + versions: 0 +- create_time: '2024-08-29' + creators: + - Wendi Bacon + doi: '' + edam_operation: [] + edam_topic: [] + id: 5b8e4ae3447934d9 + latest_version: 12 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=5b8e4ae3447934d9 + name: LOCKED | Annotating clusters + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + - name:training + tools: + - anndata_manipulate + - scanpy_plot_embed + - anndata_ops + update_time: '2024-09-01' + versions: 12 +- create_time: '2024-08-30' + creators: + - Wendi Bacon + - The Open University + - Julia Jakiela + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: f05754467a439134 + latest_version: 25 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=f05754467a439134 + name: LOCKED | Import and Analyse from EBI - Universal + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + - name:training + - name:public-data + tools: + - scanpy_read_10x + - scanpy_compute_graph + - scanpy_normalise_data + - join1 + - scanpy_filter_cells + - scanpy_find_variable_genes + - retrieve_scxa + - scanpy_scale_data + - scanpy_find_markers + - tp_grep_tool + - scanpy_run_pca + - anndata_inspect + - regexColumn1 + - scanpy_run_tsne + - scanpy_run_umap + - anndata_ops + - datamash_transpose + - scanpy_find_cluster + - scanpy_plot_embed + - scanpy_filter_genes + - scanpy_plot + update_time: '2024-09-01' + versions: 25 +- create_time: '2024-03-29' + creators: + - "Marie Joss\xE9" + doi: '' + edam_operation: [] + edam_topic: [] + id: a80f9b926ba43892 + latest_version: 15 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=a80f9b926ba43892 + name: 'Full Analyse Argo data ' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Ocean + - Pangeo + - earth-system + tools: + - xarray_metadata_info + - xarray_coords_info + - timeseries_extraction + - argo_getdata + - interactive_tool_odv + update_time: '2024-08-30' + versions: 15 +- create_time: '2024-07-02' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: 38f12705279b5dfa + latest_version: 5 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa + name: TreeValGalMay2_optionalwindowmasker + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - Add_a_column1 + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - jbrowse2 + - minimap2 + - deeptools_bam_coverage + - pick_value + - fasta_compute_length + update_time: '2024-08-28' + versions: 5 +- create_time: '2024-05-02' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: efb58bba65393347 + latest_version: 32 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=efb58bba65393347 + name: TreeValGalMay2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - Add_a_column1 + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - jbrowse2 + - minimap2 + - deeptools_bam_coverage + - pick_value + - fasta_compute_length + update_time: '2024-08-28' + versions: 32 +- create_time: '2024-08-27' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: 7f6950394a8c9c4a + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a + name: Vole to Mice Workflow Trial + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - promoter2 + - edu.tamu.cpt.genbank.shinefind + - jbrowse + - iframe + - create_or_update + - blast_reciprocal_best_hits + - get_orfs_or_cdss + update_time: '2024-08-28' + versions: 3 +- create_time: '2024-08-23' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: ddced7b107e4707a + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=ddced7b107e4707a + name: Workflow constructed from history '3k1' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - anndata_manipulate + - anndata_inspect + - tp_cat + - scanpy_plot + - scanpy_inspect + update_time: '2024-08-23' + versions: 0 +- create_time: '2024-03-25' + creators: + - MGnify - EMBL + - Rand Zoabi + - Paul Zierep + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b7166aff73e5d81c + latest_version: 13 + license: Apache-2.0 + link: https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c + name: MGnify's amplicon pipeline v5.0 - Quality control SE + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MGnify_Amplicon + - amplicon + - metagenomics + tools: + - fastqc + - trimmomatic + - fastq_filter + - cshl_fasta_formatter + - fastq_to_fasta_python + - prinseq + - tp_find_and_replace + - multiqc + update_time: '2024-08-21' + versions: 13 +- create_time: '2024-05-06' + creators: + - EMBL's European Bioinformatics Institute + - Rand Zoabi + - Paul Zierep + doi: '' + edam_operation: + - Mapping + - Formatting + - Visualisation + - k-mer counting + edam_topic: [] + id: 169327ba670607d1 + latest_version: 23 + license: Apache-2.0 + link: https://usegalaxy.eu/published/workflow?id=169327ba670607d1 + name: MGnify's amplicon pipeline v5.0 - ITS + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MGnify_Amplicon + - amplicon + - metagenomics + tools: + - collection_element_identifiers + - taxonomy_krona_chart + - biom_convert + - bedtools_maskfastabed + - tp_awk_tool + - __FILTER_FROM_FILE__ + - __FILTER_EMPTY_DATASETS__ + - mapseq + update_time: '2024-08-21' + versions: 23 +- create_time: '2024-05-27' + creators: + - EMBL's European Bioinformatics Institute + - Rand Zoabi + - Paul Zierep + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Nucleic acid design + - Sequencing quality control + edam_topic: [] + id: f9648091c06171cd + latest_version: 14 + license: Apache-2.0 + link: https://usegalaxy.eu/published/workflow?id=f9648091c06171cd + name: MGnify's amplicon pipeline v5.0 - Quality control PE + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MGnify_Amplicon + - amplicon + - metagenomics + tools: + - fastqc + - fastp + - trimmomatic + - __UNZIP_COLLECTION__ + - fastq_filter + - cshl_fasta_formatter + - fastq_to_fasta_python + - prinseq + - tp_find_and_replace + - multiqc + - mgnify_seqprep + update_time: '2024-08-21' + versions: 14 +- create_time: '2024-05-06' + creators: + - EMBL's European Bioinformatics Institute + - Rand Zoabi + - Paul Zierep + doi: '' + edam_operation: + - Formatting + - Visualisation + - k-mer counting + - Nucleic acid feature detection + - Comparison + - Alignment + - Mapping + edam_topic: [] + id: 0c3eee883f5ab977 + latest_version: 29 + license: Apache-2.0 + link: https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977 + name: MGnify's amplicon pipeline v5.0 - rRNA prediction + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MGnify_Amplicon + - metagenomics + - amplicon + tools: + - cmsearch_deoverlap + - gops_concat_1 + - collection_element_identifiers + - cshl_fasta_formatter + - taxonomy_krona_chart + - query_tabular + - biom_convert + - tp_awk_tool + - __FILTER_FROM_FILE__ + - __FILTER_EMPTY_DATASETS__ + - bedtools_getfastabed + - infernal_cmsearch + - mapseq + update_time: '2024-08-21' + versions: 29 +- create_time: '2024-05-06' + creators: + - ' EMBL''s European Bioinformatics Institute' + - Rand Zoabi + - Paul Zierep + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 02f90a96d01fed4f + latest_version: 79 + license: Apache-2.0 + link: https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f + name: MGnify's amplicon pipeline v5.0 - complete + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MGnify_Amplicon + - metagenomics + - amplicon + tools: + - __MERGE_COLLECTION__ + - fasterq_dump + update_time: '2024-08-21' + versions: 79 +- create_time: '2024-08-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f1309010689eb98a + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f1309010689eb98a + name: EncyclopeDIA Standard Workflow (mzML inputs) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - encyclopedia_quantify + - encyclopedia_searchtolib + update_time: '2024-08-21' + versions: 1 +- create_time: '2024-08-20' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 5d4e4b9f07a1ec20 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20 + name: Aug20 EncyclopeDIA raw inputs + number_of_steps: null + source: https://usegalaxy.eu + tags: + - proteomics + tools: + - encyclopedia_quantify + - encyclopedia_searchtolib + - msconvert + update_time: '2024-08-20' + versions: 2 +- create_time: '2023-10-26' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Taxonomic classification + - Sequence alignment analysis + - Phylogenetic tree generation + - Local alignment + - Global alignment + - Phylogenetic tree visualisation + - Variant calling + - Validation + - Sequence contamination filtering + - Sequence analysis + - Antimicrobial resistance prediction + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2c79eee5ca5a3b09 + latest_version: 47 + license: AGPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09 + name: TB Variant Analysis v1.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - pathogen + - tuberculosis + tools: + - __FILTER_FAILED_DATASETS__ + - mosdepth + - snippy + - collection_element_identifiers + - kraken2 + - __FLATTEN__ + - multiqc + - tb_profiler_profile + - fastp + - tp_cat + - tp_sed_tool + - qualimap_bamqc + - tp_awk_tool + - param_value_from_file + - bcftools_consensus + - 'EMBOSS: seqret84' + - tbvcfreport + - tb_variant_filter + - Paste1 + update_time: '2024-08-19' + versions: 47 +- create_time: '2024-08-16' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + - Phylogenetic analysis + - Sequence analysis + - Formatting + edam_topic: [] + id: e97b938ca4723827 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e97b938ca4723827 + name: Workflow constructed For drawing phylogenic tree for EBOLA virus + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snp_dists + - iqtree + - picard_NormalizeFasta + - rbc_mafft + update_time: '2024-08-17' + versions: 1 +- create_time: '2024-08-17' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + edam_topic: [] + id: d102a20c31d4673c + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=d102a20c31d4673c + name: Workflow constructed For EBOLA virus (RAxML) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - gd_raxml + - rbc_mafft + update_time: '2024-08-17' + versions: 0 +- create_time: '2024-08-15' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Taxonomic classification + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Phylogenetic tree editing + - Multiple sequence alignment + - Phylogenetic inference + - Phylogenetic tree reconstruction + edam_topic: [] + id: ec50dd6d56f50db1 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1 + name: Workflow constructed from history 'EboV Phylogenetic tree' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - newick_display + - graphlan + - gd_raxml + - rbc_mafft + update_time: '2024-08-15' + versions: 0 +- create_time: '2024-08-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Coding region prediction + - Genome annotation + - Visualisation + - Gene prediction + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: a847773b563b2328 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=a847773b563b2328 + name: Bacterial genome assembly-annotation-for MSc students (imported from uploaded + file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - quast + - spades + - prokka + - bandage_image + update_time: '2024-08-13' + versions: 0 +- create_time: '2023-06-30' + creators: + - Engy Nasr + - Paul Zierep + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Sequence composition calculation + - Primer removal + - Aggregation + - Validation + - Analysis + - Sequence trimming + - Visualisation + - Sequence feature detection + - DNA barcoding + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 466bdd8ba7b67264 + latest_version: 69 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 + name: pAllori Amplicon 16S Pre-Processing and Taxonomy Classification + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:16s + - name:metagenomics + - name:pallori + tools: + - fastqc + - collection_column_join + - trimmomatic + - taxonomy_krona_chart + - unzip + - krakentools_kreport2krona + - ampvis2_ordinate + - ampvis2_load + - tp_cut_tool + - kraken2 + - cutadapt + - __FLATTEN__ + - ampvis2_heatmap + - lotus2 + - multiqc + update_time: '2024-08-13' + versions: 69 +- create_time: '2024-08-05' + creators: + - RECETOX SpecDat + doi: '' + edam_operation: [] + edam_topic: [] + id: 4e9a2e12467bc02e + latest_version: 2 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4e9a2e12467bc02e + name: End-to-end EI+ mass spectra prediction workflow using QCxMS + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Exposomics + - QCxMS + - GC-MS + - Metabolomics + tools: + - qcxms_getres + - split_file_to_collection + - tp_cat + - xtb_molecular_optimization + - qcxms_neutral_run + - __FILTER_FAILED_DATASETS__ + - ctb_im_conformers + - tp_cut_tool + - qcxms_production_run + - param_value_from_file + - openbabel_compound_convert + update_time: '2024-08-12' + versions: 2 +- create_time: '2024-08-09' + creators: + - "Marie Joss\xE9" + doi: '' + edam_operation: + - Protein feature detection + - Genome annotation + - Sequence motif recognition + edam_topic: [] + id: b9c938d1af08124b + latest_version: 5 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b + name: Marine Omics identifying biosynthetic gene clusters + number_of_steps: null + source: https://usegalaxy.eu + tags: + - earth-system + - Ocean + - Marineomics + tools: + - interproscan + - prodigal + - regex1 + - sanntis_marine + update_time: '2024-08-09' + versions: 5 +- create_time: '2024-08-02' + creators: + - Timon Schlegel + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: e4e969e9943cdaa5 + latest_version: 10 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5 + name: Standard processing of single cell ATAC-seq data with SnapATAC2 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - scATAC-seq + - epigenetics + - name:single-cell + tools: + - anndata_manipulate + - scanpy_filter + - snapatac2_preprocessing + - snapatac2_plotting + - anndata_inspect + - Cut1 + - scanpy_normalize + - scanpy_plot + - replace_column_with_key_value_file + - anndata_ops + - snapatac2_clustering + - scanpy_inspect + update_time: '2024-08-08' + versions: 10 +- create_time: '2024-06-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 15cb6b690d23e6ef + latest_version: 29 + license: null + link: https://usegalaxy.eu/published/workflow?id=15cb6b690d23e6ef + name: Differential peak analysis with SnapATAC2 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - epigenetics + - scATAC-seq + - name:single-cell + tools: + - snapatac2_plotting + - snapatac2_peaks_and_motif + update_time: '2024-08-08' + versions: 29 +- create_time: '2024-07-31' + creators: + - '' + - Saim Momin + doi: '' + edam_operation: + - Taxonomic classification + - Genome assembly + - Phylogenetic tree generation + - Genome indexing + - Multilocus sequence typing + - Genome alignment + - Aggregation + - Phylogenetic tree visualisation + - Sequence contamination filtering + - Variant calling + - Visualisation + - Genome annotation + - Antimicrobial resistance prediction + - Validation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fde21b5f5c169114 + latest_version: 14 + license: AGPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114 + name: '[WGSBAC] Salmonella characterization from short-reads WGS data' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Salmonella + - VETLAB + tools: + - fastp + - quast + - snippy + - abricate + - bakta + - collapse_dataset + - Cut1 + - shovill + - abricate_summary + - krakentools_kreport2krona + - taxonomy_krona_chart + - sistr_cmd + - mlst + - kraken2 + - multiqc + - Filter1 + - amrfinderplus + - seqsero2 + update_time: '2024-08-02' + versions: 14 +- create_time: '2024-08-02' + creators: + - '' + - Saim Momin + doi: '' + edam_operation: + - Taxonomic classification + - Genome assembly + - Phylogenetic tree generation + - Multilocus sequence typing + - Aggregation + - Phylogenetic tree visualisation + - Sequence contamination filtering + - Variant calling + - Visualisation + - Genome annotation + - Antimicrobial resistance prediction + - Validation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 309fc4fc2e0da89c + latest_version: 5 + license: AGPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c + name: '[WGSBAC] Brucella characterization from short-reads WGS data' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Brucella + - VETLAB + tools: + - fastp + - quast + - snippy + - abricate + - bakta + - taxonomy_krona_chart + - shovill + - krakentools_kreport2krona + - mlst + - kraken2 + - multiqc + - abricate_summary + - amrfinderplus + - Filter1 + update_time: '2024-08-02' + versions: 5 +- create_time: '2024-07-28' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - De-novo assembly + - Genome alignment + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Data retrieval + - Generation + - Filtering + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 629e57958afed44c + latest_version: 9 + license: AGPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=629e57958afed44c + name: Capripox isolate subtyping and consensus genome generation from WGS data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CaPV + - VETLAB + - virology + tools: + - fastp + - read_it_and_keep + - __EXTRACT_DATASET__ + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - vapor + - qualimap_bamqc + - fasta_regex_finder + - __FLATTEN__ + - tp_find_and_replace + - ivar_consensus + - samtools_view + - param_value_from_file + - multiqc + - Show beginning1 + - bwa_mem + update_time: '2024-08-02' + versions: 9 +- create_time: '2024-08-02' + creators: + - Viktoria Isabel Schwarz + - Wolfgang Maier + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Genome indexing + - Read mapping + - Global alignment + - Validation + - Sequence contamination filtering + - Sequence analysis + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a31100610fba17a1 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a31100610fba17a1 + name: Pox Virus Illumina Amplicon Workflow from half-genomes + number_of_steps: null + source: https://usegalaxy.eu + tags: + - pox + - virology + tools: + - 'EMBOSS: maskseq51' + - split_file_to_collection + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - fasta_compute_length + - collection_element_identifiers + - datamash_ops + - Grep1 + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - samtools_merge + - tp_cat + - tp_sed_tool + - __SORTLIST__ + - qualimap_bamqc + - __APPLY_RULES__ + - param_value_from_file + - bwa_mem + - Cut1 + - __ZIP_COLLECTION__ + - ivar_consensus + - samtools_view + update_time: '2024-08-02' + versions: 0 +- create_time: '2023-07-02' + creators: + - Engy Nasr + - Paul Zierep + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Read summarisation + - RNA-Seq quantification + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ca9d3233b0912765 + latest_version: 37 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 + name: pAllori Blood RNA + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:pallori + - name:BloodRNA + - name:UMI + - name:Barcode + - name:transcriptomics + tools: + - fastqc + - collection_column_join + - __FILTER_FAILED_DATASETS__ + - umi_tools_extract + - __FLATTEN__ + - rna_star + - multiqc + - featurecounts + update_time: '2024-07-29' + versions: 37 +- create_time: '2024-07-16' + creators: + - Engy Nasr + - Paul Zierep + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Read mapping + - Validation + - Variant calling + - Visualisation + - Antimicrobial resistance prediction + - Sequencing quality control + edam_topic: [] + id: 4f245ac304ab76d9 + latest_version: 16 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9 + name: pAllori WGS + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:pallori + - name:microGalaxy + - name:WGS + tools: + - fastqc + - abricate + - trimmomatic + - collection_column_join + - Remove beginning1 + - snpSift_filter + - shovill + - bcftools_view + - ggplot2_heatmap + - regexColumn1 + - Grouping1 + - vcf2tsv + - bcftools_norm + - tp_awk_tool + - __FLATTEN__ + - multiqc + - bowtie2 + - freebayes + update_time: '2024-07-28' + versions: 16 +- create_time: '2024-07-26' + creators: + - Wolfgang Maier + - Viktoria Isabel Schwarz + doi: '' + edam_operation: + - Phylogenetic analysis + - Data handling + - Sequence alignment analysis + - De-novo assembly + - Genome indexing + - Sequence file editing + - Read mapping + - Sequence contamination filtering + - Sequence analysis + - Base position variability plotting + - Generation + - Data retrieval + - Multiple sequence alignment + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bc5ced57e711acf9 + latest_version: 21 + license: AGPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9 + name: Influenza sequence data analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - AIV + - VETLAB + - virology + tools: + - __UNZIP_COLLECTION__ + - __EXTRACT_DATASET__ + - collapse_dataset + - rbc_mafft + - __RELABEL_FROM_FILE__ + - tp_find_and_replace + - iqtree + - collection_element_identifiers + - bamtools_split_ref + - Grep1 + - vapor + - fastp + - __DUPLICATE_FILE_TO_COLLECTION__ + - snipit + - qualimap_bamqc + - __APPLY_RULES__ + - seqtk_subseq + - param_value_from_file + - pick_value + - Show beginning1 + - bwa_mem + - map_param_value + - wc_gnu + - Paste1 + - ivar_consensus + - samtools_view + update_time: '2024-07-28' + versions: 21 +- create_time: '2024-07-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c278d2168c28b9c3 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=c278d2168c28b9c3 + name: alphafold_biopython_alignandRMSD + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - biopdb_align_and_rmsd + - alphafold + update_time: '2024-07-19' + versions: 2 +- create_time: '2023-11-15' + creators: [] + doi: '' + edam_operation: + - Genome comparison + - Statistical calculation + - Genome assembly + - Local alignment + - Sequence composition calculation + - Read mapping + - Read binning + - Validation + - Genome annotation + - Visualisation + - Sequence clustering + - Sequence assembly + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 97312d273b6e8bd9 + latest_version: 14 + license: null + link: https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 + name: MAGs workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + tools: + - __UNZIP_COLLECTION__ + - drep_dereplicate + - concoct_extract_fasta_bins + - bowtie2 + - concoct_merge_cut_up_clustering + - samtools_sort + - checkm_lineage_wf + - concoct + - metabat2_jgi_summarize_bam_contig_depths + - semibin + - fastq_paired_end_interlacer + - megahit + - maxbin2 + - quast + - metabat2 + - concoct_coverage_table + - das_tool + - Fasta_to_Contig2Bin + - concoct_cut_up_fasta + - coverm_genome + update_time: '2024-07-11' + versions: 14 +- create_time: '2024-07-08' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 84a55e1bd760fa1e + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=84a55e1bd760fa1e + name: Unnamed Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_plot + - scanpy_cluster_reduce_dimension + - scanpy_inspect + update_time: '2024-07-08' + versions: 0 +- create_time: '2024-05-31' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: [] + edam_topic: [] + id: 0dce37adb369492c + latest_version: 93 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0dce37adb369492c + name: PathoGFAIR + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:IWC + - name:PathoGFAIR + - name:Nanopore + - name:Collection + tools: [] + update_time: '2024-07-03' + versions: 93 +- create_time: '2024-06-26' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: c7f34c67c9054234 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234 + name: Data Submission Workflow 2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - compress_file + - fastq_filter + - collection_element_identifiers + - __FILTER_FAILED_DATASETS__ + - regex_replace + - __RELABEL_FROM_FILE__ + - cutadapt + - tp_sorted_uniq + - Paste1 + - ab1_fastq_converter + - __FILTER_EMPTY_DATASETS__ + - multiqc + - ncbi_blastn_wrapper + update_time: '2024-07-03' + versions: 6 +- create_time: '2024-07-02' + creators: + - Center for Phage Technology, Texas A&M University + - Jason Gill + doi: '' + edam_operation: + - Protein feature detection + - Genome visualisation + - Sequence motif recognition + edam_topic: [] + id: df7d9943423549df + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=df7d9943423549df + name: CPT Phage Functional Workflow v2024.2 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CPT + - phage + - Apollo + tools: + - edu.tamu.cpt.fasta.remove_desc + - ncbi_blastp_wrapper + - blastxml_to_gapped_gff3 + - cshl_fasta_formatter + - gff3.rebase + - edu.tamu.cpt.fasta.lipory + - edu.tamu.cpt.gff3.cdsParents + - edu.tamu.cpt.gff3.remove_annots + - interproscan + - edu.tamu.cpt.gff3.require_phage_start + - edu.tamu.cpt.gff3.export_seq + - edu.tamu.cpt.fasta.seq_trans + - fetch_jbrowse + - jbrowse + - iframe + - create_or_update + - get_orfs_or_cdss + update_time: '2024-07-02' + versions: 1 +- create_time: '2024-07-02' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: bf655ab3dc6fd76a + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=bf655ab3dc6fd76a + name: FeaturesInExons + number_of_steps: null + source: https://usegalaxy.eu + tags: + - EEBG24 + tools: + - sort1 + - datamash_ops + - tp_easyjoin_tool + - bedtools_intersectbed + - Show beginning1 + update_time: '2024-07-02' + versions: 2 +- create_time: '2024-05-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ab89c61db3d7abbb + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=ab89c61db3d7abbb + name: "Workflow constructed from history 'Tuto EML Assembly Line \xE9tape 5 : Cr\xE9\ + ation d'EML \xE0 partir de fichiers g\xE9n\xE9tiques'" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_cat + - makeeml + - fasta2tab + - __BUILD_LIST__ + - __MERGE_COLLECTION__ + - eal_table_template + update_time: '2024-07-01' + versions: 0 +- create_time: '2021-09-29' + creators: [] + doi: '' + edam_operation: + - Read mapping + - Nucleic acid sequence analysis + edam_topic: [] + id: 006ea49456a2a8ca + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=006ea49456a2a8ca + name: 210928_reads+100bp-readlength_post-demux-minalignment-qual=5,scoring function,extension + attempts, reeeding + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - bowtie2 + - htseq_count + update_time: '2024-06-30' + versions: 3 +- create_time: '2021-04-22' + creators: [] + doi: '' + edam_operation: + - Read mapping + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 0821ec1cb4d6f30b + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=0821ec1cb4d6f30b + name: ' 210422_post-demux-reads+UMI-naming_100bp-readlength' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - bowtie2 + - htseq_count + - umi_tools_count + update_time: '2024-06-30' + versions: 1 +- create_time: '2023-12-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Data handling + - Gene functional annotation + - Sequence composition calculation + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 20ada53472782c9b + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=20ada53472782c9b + name: Wormflow_Example_RNAseq_goseq + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - join1 + - __RELABEL_FROM_FILE__ + - tp_replace_in_column + - __TAG_FROM_FILE__ + - featurecounts + - rseqc_junction_annotation + - collection_element_identifiers + - Remove beginning1 + - samtools_idxstats + - ggplot2_heatmap2 + - cat1 + - Convert characters1 + - rna_star + - multiqc + - deseq2 + - sort1 + - gtftobed12 + - tp_replace_in_line + - Add_a_column1 + - volcanoplot + - Show beginning1 + - Filter1 + - Cut1 + - rseqc_read_distribution + - goseq + update_time: '2024-06-29' + versions: 4 +- create_time: '2024-05-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e95bfab07fdec632 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=e95bfab07fdec632 + name: Workflow constructed from history 'Open Science Persistent Demonstrator Example' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - zoo_project_ogc_api_processes + update_time: '2024-06-25' + versions: 5 +- create_time: '2024-04-03' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Visualisation + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Mapping + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: 376119528377a3ae + latest_version: 58 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=376119528377a3ae + name: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - collection_column_join + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - ggplot2_heatmap + - fasta2tab + - tp_replace_in_column + - tp_sorted_uniq + - clustalw + - Remove beginning1 + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - tp_split_on_column + - newick_display + - Count1 + - regexColumn1 + - bedtools_getfastabed + - tp_multijoin_tool + - Cut1 + - fasttree + - tab2fasta + - __FILTER_EMPTY_DATASETS__ + - regex1 + update_time: '2024-06-24' + versions: 58 +- create_time: '2023-04-12' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Variant calling + - Pairwise sequence alignment + edam_topic: [] + id: 09c7069ae409c362 + latest_version: 72 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=09c7069ae409c362 + name: Allele-based Pathogen Identification + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - clair3 + - CONVERTER_gz_to_uncompressed + - table_compute + - snpSift_filter + - Count1 + - Remove beginning1 + - Cut1 + - snpSift_extractFields + - collapse_dataset + - samtools_coverage + - regexColumn1 + - tp_cut_tool + - bcftools_norm + - tp_head_tool + - samtools_depth + - Paste1 + - minimap2 + - bcftools_consensus + update_time: '2024-06-24' + versions: 72 +- create_time: '2023-04-12' + creators: + - "B\xE9r\xE9nice Batut" + - Engy Nasr + - Paul Zierep + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Visualisation + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: a705370bc2c13d5c + latest_version: 190 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c + name: Nanopore Preprocessing + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:Nanopore + - name:IWC + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - krakentools_extract_kraken_reads + - collection_column_join + - Cut1 + - collapse_dataset + - Add_a_column1 + - __FILTER_FAILED_DATASETS__ + - bamtools_split_mapped + - regexColumn1 + - kraken2 + - porechop + - Grep1 + - minimap2 + - multiqc + update_time: '2024-06-24' + versions: 190 +- create_time: '2023-04-12' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Taxonomic classification + edam_topic: [] + id: b67b5ecd3305f830 + latest_version: 8 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830 + name: Taxonomy Profiling and Visualization with Phinch + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:collection + - name:microGalaxy + - name:GTN + tools: + - kraken2 + - interactive_tool_phinch + - kraken_biom + update_time: '2024-06-19' + versions: 8 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Formatting + - Visualisation + - Prediction and recognition + - Filtering + - Label-free quantification + edam_topic: [] + id: fc42cc9467c6ee8d + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d + name: metaQuantome_datacreation_workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - proteomics + - name:microGalaxy + tools: + - Remove beginning1 + - Cut1 + - tp_replace_in_line + - query_tabular + - tp_replace_in_column + - flashlfq + - peptide_shaker + - search_gui + - unipept + - msconvert + - regex1 + - Filter1 + update_time: '2024-06-19' + versions: 0 +- create_time: '2024-06-10' + creators: + - "Computer Research Institute of Montr\xE9al (CRIM)" + - Francis Charette-Migneault + doi: '' + edam_operation: [] + edam_topic: [] + id: b1fa4a3561988704 + latest_version: 15 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704 + name: CRIM-GeoLabs Turbidity Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Sentinel-2 + - Turbidity + - CRIM + - GeoLabs + - OGCAPI-Processes + - OSPD + tools: + - cat1 + - otb_band_math + - hirondelle_crim + update_time: '2024-06-19' + versions: 15 +- create_time: '2024-06-12' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: e2af8c661e98f4f4 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4 + name: 'QIIME2 V: Taxonomic analysis' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - qiime2__metadata__tabulate + - qiime2__feature_classifier__classify_sklearn + - qiime2__taxa__barplot + update_time: '2024-06-18' + versions: 1 +- create_time: '2024-06-12' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 6e5fad1de09af683 + latest_version: 2 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683 + name: 'QIIME2 VI: Diversity metrics and estimations' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - qiime2_core__tools__import + - qiime2__diversity__core_metrics_phylogenetic + - __BUILD_LIST__ + - qiime2__diversity__beta_group_significance + - qiime2__diversity__alpha_group_significance + update_time: '2024-06-18' + versions: 2 +- create_time: '2024-06-12' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 86b31ac8a7720e41 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41 + name: 'QIIME2 I: Demultiplexing (single-end)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:amplicon + - name:16S + - name:tutorial + tools: + - qiime2__demux__emp_single + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-06-18' + versions: 1 +- create_time: '2024-06-12' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: da17a4d690eb0ff3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3 + name: 'QIIME2 II: Denoising (sequence quality control) and feature table creation + (single-end)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:amplicon + - name:16S + - name:tutorial + tools: + - qiime2__feature_table__summarize + - qiime2__dada2__denoise_single + - qiime2__feature_table__tabulate_seqs + - qiime2__metadata__tabulate + update_time: '2024-06-18' + versions: 1 +- create_time: '2024-06-12' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 6ad6d87618c4e405 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6ad6d87618c4e405 + name: 'QIIME2 III: Phylogenetic tree for diversity analysis' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - qiime2__fragment_insertion__sepp + update_time: '2024-06-18' + versions: 1 +- create_time: '2024-06-08' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + edam_topic: [] + id: e522be58f0bac656 + latest_version: 9 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=e522be58f0bac656 + name: TreeValGal_Winnowmap + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - winnowmap + - bbgtobigwig + - bamFilter + - meryl + - fasta_compute_length + update_time: '2024-06-17' + versions: 9 +- create_time: '2024-06-08' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: aada0111f835ce49 + latest_version: 22 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=aada0111f835ce49 + name: TreeValGalJune9 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - Add_a_column1 + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - gff2bed1 + - jbrowse2 + - minimap2 + - deeptools_bam_coverage + - pick_value + - fasta_compute_length + update_time: '2024-06-14' + versions: 22 +- create_time: '2024-06-12' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 0d24e8ff7221c9dc + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=0d24e8ff7221c9dc + name: Copy of Workflow constructed from history 'Galaxy 101' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - CONVERTER_bed_to_fli_0 + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - CONVERTER_interval_to_bgzip_0 + - comp1 + update_time: '2024-06-12' + versions: 0 +- create_time: '2024-06-10' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 2d509fad86eb97fb + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2d509fad86eb97fb + name: 'COVID-19: variation analysis reporting (imported from uploaded file)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2024-06-10' + versions: 0 +- create_time: '2024-01-21' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 4ca06bc64bf896a3 + latest_version: 40 + license: null + link: https://usegalaxy.eu/published/workflow?id=4ca06bc64bf896a3 + name: TreeValGal bed to bigwig + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ucsc_wigtobigwig + - Cut1 + - bedtools_coveragebed + update_time: '2024-06-09' + versions: 40 +- create_time: '2024-06-06' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Structure visualisation + - Genome visualisation + - Pathway visualisation + - Data handling + - Sequence alignment analysis + edam_topic: [] + id: 2cd5670f075704ab + latest_version: 5 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab + name: winnowmap workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - winnowmap + - bamFilter + - jbrowse2 + - CONVERTER_bam_to_bigwig_0 + - meryl + update_time: '2024-06-08' + versions: 5 +- create_time: '2024-05-17' + creators: + - RECETOX SpecDat + doi: '' + edam_operation: [] + edam_topic: [] + id: 5465916d9b51f411 + latest_version: 64 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5465916d9b51f411 + name: 'End-to-end spectra predictions: multi atoms dataset' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Exposomics + - QCxMS + - GC-MS + - Metabolomics + tools: + - qcxms_getres + - xtb_molecular_optimization + - qcxms_neutral_run + - __FILTER_FAILED_DATASETS__ + - ctb_im_conformers + - qcxms_production_run + - openbabel_compound_convert + update_time: '2024-06-06' + versions: 64 +- create_time: '2023-04-13' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + edam_topic: [] + id: 585c21b7b1d864fc + latest_version: 142 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc + name: Gene-based Pathogen Identification + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:PathoGFAIR + - name:IWC + - name:microGalaxy + tools: + - abricate + - medaka_consensus_pipeline + - collection_element_identifiers + - split_file_to_collection + - flye + - fasta2tab + - bandage_image + - tab2fasta + - compose_text_param + - tp_find_and_replace + - __BUILD_LIST__ + - param_value_from_file + update_time: '2024-06-05' + versions: 142 +- create_time: '2023-05-11' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: 10101558b211a782 + latest_version: 58 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=10101558b211a782 + name: Taxonomy Profiling and Visualization with Krona + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - kraken2 + - krakentools_kreport2krona + - taxonomy_krona_chart + update_time: '2024-06-05' + versions: 58 +- create_time: '2024-05-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 290373b2f5fb8c6c + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c + name: Workflow constructed from history 'Tool based FPE' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seurat_filter_cells + - seurat_run_umap + - seurat_find_variable_genes + - seurat_run_pca + - seurat_find_neighbours + - seurat_read10x + - seurat_find_clusters + - seurat_scale_data + - seurat_plot + - seurat_normalise_data + - retrieve_scxa + update_time: '2024-06-03' + versions: 0 +- create_time: '2024-05-29' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9eda857e4141d56e + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9eda857e4141d56e + name: Generic variation analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - mpxv + - generic + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-05-29' + versions: 0 +- create_time: '2024-05-29' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: cd926dd6b70e72d6 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=cd926dd6b70e72d6 + name: Generic variation analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - mpxv + - generic + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-05-29' + versions: 0 +- create_time: '2024-05-14' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 529f30e894beacc2 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=529f30e894beacc2 + name: 'Copy of COVID-19: variation analysis of ARTIC ONT (release v0.3) shared by + user iwc' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2024-05-29' + versions: 0 +- create_time: '2024-05-28' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 112422839b68db02 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=112422839b68db02 + name: Variant analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - mpxv + - generic + - cloud-costs + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-05-28' + versions: 0 +- create_time: '2024-05-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 67e20e3082d24fbd + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd + name: Workflow For RNA-Seq Analysis of LATS1/2 depletion + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - join1 + - salmon + - column_order_header_sort + - tp_tail_tool + - tp_cut_tool + - Grep1 + - limma_voom + - gprofiler_gost + - tp_find_and_replace + - ggplot2_heatmap2 + - Filter1 + update_time: '2024-05-27' + versions: 5 +- create_time: '2024-04-12' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - Sequence annotation + - Scaffolding + - Sequence analysis + - Transcriptome assembly + - Genome annotation + - RNA-Seq analysis + - Differential protein expression profiling + - Gene prediction + - Editing + - Sequence assembly validation + edam_topic: [] + id: 9fb31a16b258cc1a + latest_version: 20 + license: null + link: https://usegalaxy.eu/published/workflow?id=9fb31a16b258cc1a + name: Copy of Helixer and RED - Genome annotation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomeannotation + - Helixer + - Visualization + - Red + tools: + - compleasm + - helixer + - gffread + - jcvi_gff_stats + - red + - omark + - jbrowse + - busco + update_time: '2024-05-27' + versions: 20 +- create_time: '2023-03-01' + creators: + - Marie Josse + doi: '' + edam_operation: [] + edam_topic: [] + id: 1d2cd0af01a30a46 + latest_version: 5 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1d2cd0af01a30a46 + name: Satellite data for biodiversity + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Ecology + - earth-system + - satellite + tools: + - srs_diversity_maps + - srs_global_indices + - srs_spectral_indices + - srs_preprocess_s2 + update_time: '2024-05-27' + versions: 5 +- create_time: '2024-05-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2f37c35ade97aa8d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d + name: Workflow constructed from history 'RNA expression in Monocytes from thrombocytopenic + mice' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - join1 + - salmon + - column_order_header_sort + - tp_tail_tool + - tp_cut_tool + - Grep1 + - gprofiler_gost + - ggplot2_heatmap2 + - tp_find_and_replace + - Filter1 + - limma_voom + update_time: '2024-05-27' + versions: 1 +- create_time: '2024-05-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 21dd4bd16579fc12 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12 + name: SINGLE class_heatmap + number_of_steps: null + source: https://usegalaxy.eu + tags: + - UAM + - '2024' + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - join1 + - salmon + - __RELABEL_FROM_FILE__ + - tp_tail_tool + - tp_cut_tool + - ggplot2_heatmap2 + - gprofiler_gost + - Paste1 + - tp_find_and_replace + - Filter1 + - limma_voom + update_time: '2024-05-26' + versions: 3 +- create_time: '2021-12-20' + creators: + - PNDB + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 510bcef37f385495 + latest_version: 4 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=510bcef37f385495 + name: Intrapsecific genetic diversity, genetic differentiation and inbreeding EBV + workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - EBV + - Genetic + tools: + - fastqc + - stacks2_procrad + - tp_sort_header_tool + - stacks2_denovomap + - stacks2_populations + - tp_head_tool + - CONVERTER_bed_gff_or_vcf_to_bigwig_0 + - multiqc + - Filter1 + update_time: '2024-05-23' + versions: 4 +- create_time: '2023-05-14' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: d086340422009ba9 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=d086340422009ba9 + name: RNAseq-Mouse-Stranded-HTseqCount_20230514 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - __FLATTEN__ + - htseq_count + - multiqc + - hisat2 + update_time: '2024-05-19' + versions: 2 +- create_time: '2024-05-18' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 2fd462d85412444c + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=2fd462d85412444c + name: '''EO_HW4_RNA-Seq Exercise'' - QC' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - multiqc + - cutadapt + - __FLATTEN__ + update_time: '2024-05-18' + versions: 1 +- create_time: '2024-05-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 0ec684b341ad172d + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=0ec684b341ad172d + name: FASTQC-MULTIQC-Quality-Check_FastQ_Files + number_of_steps: null + source: https://usegalaxy.eu + tags: + - BGGM + - Microbiome + - Amplicon + - FASTQC + - QualityCheck + tools: + - fastqc + - multiqc + update_time: '2024-05-17' + versions: 8 +- create_time: '2024-04-24' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - Sequence annotation + - Scaffolding + - Sequence analysis + - Transcriptome assembly + - Genome annotation + - Differential protein expression profiling + - Repeat sequence detection + - Gene prediction + - Sequence assembly validation + edam_topic: [] + id: 4077e77b6af919c4 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4 + name: Helixer and RepeatMasker - Genome annotation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomeannotation + - Helixer + - Visualization + tools: + - compleasm + - helixer + - gffread + - jcvi_gff_stats + - repeatmasker_wrapper + - omark + - jbrowse + - repeatmodeler + - busco + update_time: '2024-05-15' + versions: 6 +- create_time: '2023-05-11' + creators: + - "B\xE9r\xE9nice Batut" + - Mallory Freeberg + - Mo Heydarian + - Anika Erxleben + - Pavankumar Videm + - Clemens Blank + - Maria Doyle + - Nicola Soranzo + - Peter van Heusden + - Lucille Delisle + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - RNA-Seq quantification + - Data handling + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Visualisation + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 985044b4b2c51425 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=985044b4b2c51425 + name: QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics + - GTN + number_of_steps: null + source: https://usegalaxy.eu + tags: + - transcriptomics + tools: + - fastqc + - pygenomeTracks + - tp_tail_tool + - featurecounts + - samtools_idxstats + - tp_sort_header_tool + - cutadapt + - __FLATTEN__ + - rseqc_infer_experiment + - rna_star + - multiqc + - __MERGE_COLLECTION__ + - gtftobed12 + - rseqc_geneBody_coverage + - length_and_gc_content + - Cut1 + - rseqc_read_distribution + - samtools_view + - picard_MarkDuplicates + update_time: '2024-05-13' + versions: 0 +- create_time: '2023-05-11' + creators: + - "B\xE9r\xE9nice Batut" + - Mallory Freeberg + - Mo Heydarian + - Anika Erxleben + - Pavankumar Videm + - Clemens Blank + - Maria Doyle + - Nicola Soranzo + - Peter van Heusden + - Lucille Delisle + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Visualisation + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a28c207730e7e13d + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d + name: QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN + number_of_steps: null + source: https://usegalaxy.eu + tags: + - transcriptomics + tools: + - fastqc + - gtftobed12 + - samtools_idxstats + - Cut1 + - tp_sort_header_tool + - pygenomeTracks + - rseqc_read_distribution + - tp_tail_tool + - rseqc_geneBody_coverage + - cutadapt + - __FLATTEN__ + - rseqc_infer_experiment + - rna_star + - multiqc + - picard_MarkDuplicates + - featurecounts + - length_and_gc_content + update_time: '2024-05-13' + versions: 0 +- create_time: '2024-05-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fe64d430d50faf0b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b + name: "Workflow constructed from history 'TRANSCRIPT\xD3MICA, REGULACI\xD3N GEN\xD3\ + MICA Y EPIGEN\xD3MICA'" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - join1 + - salmon + - column_order_header_sort + - tp_tail_tool + - tp_cut_tool + - Grep1 + - limma_voom + - gprofiler_gost + - tp_find_and_replace + - ggplot2_heatmap2 + - Filter1 + update_time: '2024-05-08' + versions: 0 +- create_time: '2024-05-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6fc2b9bea5b75a49 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49 + name: SilvanaRuizGalaxy + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - join1 + - salmon + - column_order_header_sort + - tp_tail_tool + - tp_cut_tool + - Grep1 + - limma_voom + - gprofiler_gost + - tp_find_and_replace + - ggplot2_heatmap2 + - Filter1 + update_time: '2024-05-08' + versions: 0 +- create_time: '2024-04-30' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Sequence contamination filtering + - Formatting + - Statistical calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a2d4221ad117c378 + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=a2d4221ad117c378 + name: Allelic Imbalance PLN R14del t2t + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - vcfcombine + - Add_a_column1 + - picard_AddOrReplaceReadGroups + - vcf2tsv + - snpEff + - tp_unfold_column_tool + - rna_star + - snpSift_annotate + - Filter1 + - freebayes + update_time: '2024-05-08' + versions: 13 +- create_time: '2024-02-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Primer removal + - Sequence contamination filtering + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: b6eb5fe7e37f680a + latest_version: 24 + license: null + link: https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a + name: C. vibrioides Alignment + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastp + - trimmomatic + - trim_galore + - fastq_dump + - fastq_quality_trimmer + - sickle + - samtools_stats + - htseq_count + - hisat2 + update_time: '2024-05-08' + versions: 24 +- create_time: '2024-04-23' + creators: + - Riccardo Massei + doi: '' + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: e87e726b57f1a875 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=e87e726b57f1a875 + name: Manual Threshold Tester + number_of_steps: null + source: https://usegalaxy.eu + tags: + - imageanaylsis + - threshold + - preprocessing + tools: + - param_value_from_file + - ip_threshold + - tp_split_on_column + update_time: '2024-05-05' + versions: 4 +- create_time: '2024-04-22' + creators: + - Riccardo Massei + doi: '' + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: 1ffacb28226460ac + latest_version: 9 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac + name: Generic Nuclei Segmentation and Feature Extraction + number_of_steps: null + source: https://usegalaxy.eu + tags: + - imageanaylsis + - nuclei + - Segmentation + tools: + - ip_threshold + - ip_convertimage + - ip_overlay_images + - ip_count_objects + - ip_binary_to_labelimage + - ip_2d_filter_segmentation_by_features + - ip_filter_standard + - ip_2d_feature_extraction + - ip_histogram_equalization + update_time: '2024-05-05' + versions: 9 +- create_time: '2024-04-30' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: 5f29105e842716db + latest_version: 40 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5f29105e842716db + name: TreeValGalAprill30 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - Add_a_column1 + - mashmap + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - jbrowse2 + - minimap2 + - deeptools_bam_coverage + - pick_value + - fasta_compute_length + update_time: '2024-05-02' + versions: 40 +- create_time: '2024-04-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5aaa64ecdf9f7d6e + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=5aaa64ecdf9f7d6e + name: TreeValGalSimilarity + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mashmap + - pick_value + update_time: '2024-05-01' + versions: 9 +- create_time: '2024-04-24' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: 3cf3dd9727b7ac92 + latest_version: 26 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92 + name: TreeValGalApril24 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - Add_a_column1 + - mashmap + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - jbrowse2 + - minimap2 + - deeptools_bam_coverage + - pick_value + - fasta_compute_length + update_time: '2024-04-27' + versions: 26 +- create_time: '2024-04-25' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Statistical calculation + - Formatting + - Sequence profile generation + - Format validation + - Sequence motif recognition + - Primer removal + - Aggregation + - Coding region prediction + - Sequence assembly + - Data retrieval + - Sequence assembly validation + - Sequencing quality control + - Protein feature detection + - Taxonomic classification + - Gene functional annotation + - Local alignment + - Sequence composition calculation + - Database search + - Validation + - Sequence trimming + - Visualisation + - Sequence analysis + - Conversion + - Probabilistic sequence generation + - Multiple sequence alignment + - Sequence generation + - Gene prediction + - Read pre-processing + edam_topic: [] + id: 8deb08d4f228e198 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198 + name: Metawin + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fasplit + - krakentools_kreport2krona + - fraggenescan + - taxonomy_krona_chart + - trim_galore + - checkm_lineage_wf + - kraken2 + - tp_grep_tool + - coverm_contig + - cat_bins + - sort1 + - tp_cat + - tp_awk_tool + - maxbin2 + - quast + - hmmer_hmmscan + - interproscan + - kofamscan + - coverm_genome + update_time: '2024-04-25' + versions: 1 +- create_time: '2021-08-14' + creators: [] + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Visualisation + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly validation + - Scatter plot plotting + edam_topic: [] + id: 34a07bf6407510ef + latest_version: 15 + license: null + link: https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef + name: Nanopore genome sequencing + number_of_steps: null + source: https://usegalaxy.eu + tags: + - WGS + - Nanopore + tools: + - quast + - nanoplot + - medaka_consensus_pipeline + - flye + update_time: '2024-04-24' + versions: 15 +- create_time: '2024-04-19' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: 2e93613c688ea52e + latest_version: 34 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e + name: TreeValGalApril19 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - Add_a_column1 + - mashmap + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - jbrowse2 + - minimap2 + - deeptools_bam_coverage + - pick_value + - fasta_compute_length + update_time: '2024-04-23' + versions: 34 +- create_time: '2024-02-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5c7a9738cbc10897 + latest_version: 20 + license: null + link: https://usegalaxy.eu/published/workflow?id=5c7a9738cbc10897 + name: Scannotation_input_files + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Scannotation + - XCMS + tools: + - tp_cut_tool + - join1 + - tp_find_and_replace + update_time: '2024-04-22' + versions: 20 +- create_time: '2024-04-01' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: cc2bc81352d2e2cd + latest_version: 20 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd + name: TreeValGalApril2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - mashmap + - Add_a_column1 + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - jbrowse2 + - minimap2 + - deeptools_bam_coverage + - fasta_compute_length + update_time: '2024-04-19' + versions: 20 +- create_time: '2024-04-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: af472984b3f3d65f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=af472984b3f3d65f + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-04-18' + versions: 1 +- create_time: '2024-04-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 8c4331f1bac67aba + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=8c4331f1bac67aba + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-04-18' + versions: 1 +- create_time: '2024-04-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 895b8f5736bb92bb + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=895b8f5736bb92bb + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-04-18' + versions: 1 +- create_time: '2024-04-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 4fe19f3eac3b28ab + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4fe19f3eac3b28ab + name: Parallel Accession Down (release v0.1.12) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-04-18' + versions: 1 +- create_time: '2024-03-12' + creators: [] + doi: '' + edam_operation: + - Scaffolding + - Transcriptome assembly + - Sequence assembly validation + - Genome assembly + edam_topic: [] + id: c9a8fba4c56f5c83 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c9a8fba4c56f5c83 + name: Snail plot using 'BlobToolKit' (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - blobtoolkit + - busco + - interactive_tool_blobtoolkit + update_time: '2024-04-17' + versions: 0 +- create_time: '2024-04-16' + creators: [] + doi: '' + edam_operation: + - Protein feature detection + - Sequence motif recognition + edam_topic: [] + id: 9a95556ec171d405 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=9a95556ec171d405 + name: CPT Export genome and annotations from Galaxy v2024.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CPT + - phage + tools: + - gbk_to_orf + - edu.tamu.cpt.gff.gff2gb + - ncbi_blastp_wrapper + - interproscan + update_time: '2024-04-16' + versions: 5 +- create_time: '2024-02-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a1518a029132ee3d + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=a1518a029132ee3d + name: Phage gene finder + number_of_steps: null + source: https://usegalaxy.eu + tags: + - phage + - genecalling + - ORF + - novelgenes + - smallORFs + tools: + - edu.tamu.cpt.fasta.remove_desc + - edu.tamu.cpt.gff3.cdsParents + - edu.tamu.cpt.gff3.require_phage_start + - edu.tamu.cpt.gff3.export_seq + - get_orfs_or_cdss + update_time: '2024-04-15' + versions: 6 +- create_time: '2024-04-14' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Statistical calculation + - Fold recognition + - RNA-Seq quantification + - Information extraction + - Formatting + - Query and retrieval + - Differential gene expression analysis + - Genome annotation + - Read summarisation + - Sequencing quality control + - Data handling + - Sequence composition calculation + - Sequence annotation + - Homology-based gene prediction + - Validation + - RNA-Seq analysis + - Data retrieval + - Sequence alignment + edam_topic: [] + id: c5e6047b3b256b06 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06 + name: Workflow constructed from history 'Copy of 'Hexe bleomycin'' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - deg_annotate + - __TAG_FROM_FILE__ + - eggnog_mapper + - featurecounts + - collection_element_identifiers + - trimmer + - rna_star + - multiqc + - deseq2 + - Extract genomic DNA 1 + - tp_replace_in_line + - Add_a_column1 + - tp_head_tool + - comp1 + - gffread + - picard_NormalizeFasta + - Cut1 + - datasets_download_genome + - regex1 + update_time: '2024-04-14' + versions: 0 +- create_time: '2024-04-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 250e6058f160825f + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=250e6058f160825f + name: Workflow constructed from history 'ACUN RNA seq' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_element_identifiers + - __TAG_FROM_FILE__ + - trimmer + - rna_star + - multiqc + - featurecounts + - deseq2 + update_time: '2024-04-14' + versions: 0 +- create_time: '2024-03-27' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - Sequence annotation + - Scaffolding + - Sequence analysis + - Transcriptome assembly + - Genome annotation + - RNA-Seq analysis + - Differential protein expression profiling + - Gene prediction + - Editing + - Sequence assembly validation + edam_topic: [] + id: 3d604dad4f1f5b3d + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d + name: Helixer and RED - Genome annotation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomeannotation + - Helixer + - Visualization + - Red + tools: + - compleasm + - helixer + - gffread + - jcvi_gff_stats + - red + - omark + - jbrowse + - busco + update_time: '2024-04-11' + versions: 3 +- create_time: '2024-03-18' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - Sequence annotation + - Scaffolding + - Sequence analysis + - Transcriptome assembly + - Genome annotation + - Differential protein expression profiling + - Repeat sequence detection + - Gene prediction + - Sequence assembly validation + edam_topic: [] + id: 327beb1edda305ff + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=327beb1edda305ff + name: Helixer and RepeatModeler - Genome annotation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Genomeannotation + - Helixer + - Visualization + - RepeatMasker + - RepeatModeler + tools: + - compleasm + - helixer + - gffread + - jcvi_gff_stats + - repeatmasker_wrapper + - omark + - jbrowse + - repeatmodeler + - busco + update_time: '2024-04-11' + versions: 9 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: 0f563f176bb245af + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0f563f176bb245af + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: 6ed089fe65347272 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6ed089fe65347272 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 967f890c0883f72a + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=967f890c0883f72a + name: baredSC_2d_logN (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 2da3c41ad5c11c3b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2da3c41ad5c11c3b + name: baredSC_1d_logN (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 4cb25c0bb103f54f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4cb25c0bb103f54f + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 66f2a58637054c16 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=66f2a58637054c16 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 8ff9d3ad20e87819 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=8ff9d3ad20e87819 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 166eb3f14feffa1b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=166eb3f14feffa1b + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 93a7047396080fda + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=93a7047396080fda + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1c44bbaa5f4f8b54 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1c44bbaa5f4f8b54 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f6b55599db1ab056 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=f6b55599db1ab056 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 6ff3eb92d75626f6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6ff3eb92d75626f6 + name: Parallel Accession Down (release v0.1.11) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-08' + creators: [] + doi: '' + edam_operation: + - Validation + - RNA-Seq quantification + - Sequence alignment + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 3550384e7c062a60 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=3550384e7c062a60 + name: Hisat2+ Multiqc + FeatureCount + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - multiqc + - featurecounts + - hisat2 + update_time: '2024-04-08' + versions: 2 +- create_time: '2022-10-10' + creators: [] + doi: '' + edam_operation: + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Sequence alignment + edam_topic: [] + id: 0d6bed63a2e4c3d6 + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=0d6bed63a2e4c3d6 + name: BAM/SPLICE JUNCTION + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - trimmomatic + - samtools_sort + - fasterq_dump + - salmon + - rna_star + update_time: '2024-04-08' + versions: 9 +- create_time: '2024-04-07' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 4c0000eb4995a310 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=4c0000eb4995a310 + name: Exploring Iris dataset with statistics and scatterplots + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2024-04-07' + versions: 2 +- create_time: '2024-03-08' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: 44189803f223acd1 + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=44189803f223acd1 + name: CPT Interrupted Genes Workflow v2024.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CPT + - phage + - Apollo + tools: + - ncbi_blastp_wrapper + - blastxml_to_gapped_gff3 + - cshl_fasta_formatter + - edu.tamu.cpt2.phage.intron_detection + - gff3.rebase + - fetch_jbrowse + - jbrowse + - edu.tamu.cpt.fasta.seq_trans + - edu.tamu.cpt.gff3.export_seq + - iframe + - create_or_update + update_time: '2024-04-04' + versions: 11 +- create_time: '2022-11-29' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Visualisation + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Mapping + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: c8bc4af6dd3b5d02 + latest_version: 205 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02 + name: Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + - nanopore + - IWC + - name:Collection + - name:microGalaxy + tools: + - collection_column_join + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - ggplot2_heatmap + - fasta2tab + - tp_replace_in_column + - tp_sorted_uniq + - clustalw + - Remove beginning1 + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - tp_split_on_column + - newick_display + - Count1 + - regexColumn1 + - bedtools_getfastabed + - tp_multijoin_tool + - interactive_tool_jupyter_notebook + - Cut1 + - fasttree + - tab2fasta + - __FILTER_EMPTY_DATASETS__ + - regex1 + update_time: '2024-04-04' + versions: 205 +- create_time: '2024-04-04' + creators: + - Anna Syme + doi: '' + edam_operation: + - Visualisation + - Cross-assembly + - Mapping assembly + - Genome assembly + - De-novo assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 9ddb703e1db13504 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9ddb703e1db13504 + name: Genome assembly with Fly (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fasta-stats + - bandage_image + - quast + - flye + update_time: '2024-04-04' + versions: 1 +- create_time: '2024-03-30' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Pairwise sequence alignment + - Mapping + edam_topic: [] + id: 2b00b6498a2b4779 + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=2b00b6498a2b4779 + name: optional_fasta_to_bed + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + - pick_value + - bedtools_bamtobed + update_time: '2024-03-31' + versions: 11 +- create_time: '2024-03-29' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome visualisation + - Pathway visualisation + edam_topic: [] + id: 84414f3441946702 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=84414f3441946702 + name: jb2test10_tracks (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + - samtools_bam_to_cram + - jbrowse2 + update_time: '2024-03-30' + versions: 2 +- create_time: '2024-03-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c6f31fadd97f0667 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c6f31fadd97f0667 + name: A workflow demonstrating the 'Run interpolation based on IDW' tool + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - graphicsmagick_image_compare + - csv_to_tabular + - tabular_to_csv + - interpolation_run_idw_interpolation + - Filter1 + update_time: '2024-03-28' + versions: 0 +- create_time: '2024-03-28' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: f7cdaf862e6599c0 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=f7cdaf862e6599c0 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: e138640778b7414c + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=e138640778b7414c + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: caba6d3d7db648e9 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=caba6d3d7db648e9 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - busco + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 12b0bd336c76a874 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=12b0bd336c76a874 + name: Purge-duplicate-contigs-VGP6 (release v0.3.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: a53f78aa6866b811 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=a53f78aa6866b811 + name: Scaffolding-HiC-VGP8 (release v0.2.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 67be21795d403ca3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=67be21795d403ca3 + name: ChIPseq_SR (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1089e5c66dbcc1a3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3 + name: ATACseq (release v0.12) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2cf9f0e2ab5a7f8b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2cf9f0e2ab5a7f8b + name: ChIPseq_PE (release v0.7.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c0d1e965daf89006 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c0d1e965daf89006 + name: CUTandRUN (release v0.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-14' + creators: + - "Marie Joss\xE9" + doi: '' + edam_operation: [] + edam_topic: [] + id: fc33ea1679e5f1b7 + latest_version: 8 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=fc33ea1679e5f1b7 + name: 'Analyse Argo data ' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Ocean + - Pangeo + - earth-system + tools: + - xarray_metadata_info + - xarray_coords_info + - timeseries_extraction + - argo_getdata + - interactive_tool_odv + update_time: '2024-03-27' + versions: 8 +- create_time: '2024-03-23' + creators: + - Julia Jakiela + - Wendi Bacon + doi: '' + edam_operation: [] + edam_topic: [] + id: 73aa794916b91bb2 + latest_version: 4 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=73aa794916b91bb2 + name: Combining datasets after pre-processing + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:training + - name:single-cell + tools: + - anndata_manipulate + - Cut1 + - anndata_inspect + - tp_replace_in_column + - Paste1 + - anndata_ops + update_time: '2024-03-26' + versions: 4 +- create_time: '2024-03-09' + creators: [] + doi: '' + edam_operation: + - Nucleic acid sequence analysis + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 9e03cf8cd5e5de08 + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=9e03cf8cd5e5de08 + name: QuantSeq + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - cutadapt + - htseq_count + - rna_star + update_time: '2024-03-26' + versions: 13 +- create_time: '2024-01-31' + creators: + - "Marie Joss\xE9" + doi: '' + edam_operation: [] + edam_topic: [] + id: 8c868b087ef78bf9 + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=8c868b087ef78bf9 + name: Ocean's variables + number_of_steps: null + source: https://usegalaxy.eu + tags: + - earth-system + - Ocean + tools: + - interactive_tool_odv + - interactive_tool_divand + update_time: '2024-03-25' + versions: 2 +- create_time: '2024-03-03' + creators: + - Max Dubbeld, Sascha Dijkstra, Tijn Bothof, Yuri Danylko, Brandon Binns + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Genome assembly + - Sequence composition calculation + - Aggregation + - Coding region prediction + - Validation + - Genome annotation + - Visualisation + - Antimicrobial resistance prediction + - Gene prediction + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 2e0075791f7fa384 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384 + name: WorkflowTeamAssignment + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - staramr_search + - trimmomatic + - quast + - abricate + - Kraken2Tax + - unicycler + - bandage_image + - prokka + - kraken2 + - porechop + - multiqc + update_time: '2024-03-22' + versions: 2 +- create_time: '2024-03-15' + creators: [] + doi: '' + edam_operation: + - Differential binding analysis + edam_topic: [] + id: 719314fa5263b501 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=719314fa5263b501 + name: Peak calling with SEACR for RPE1 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seacr + - deeptools_bam_coverage + - diffbind + update_time: '2024-03-22' + versions: 4 +- create_time: '2024-03-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2addb042071557e3 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=2addb042071557e3 + name: CPT Phage DNA comparative workflow v2024.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CPT + - phage + - Apollo + tools: + - edu.tamu.cpt.blast.relatedness.nuc + - ncbi_blastn_wrapper + update_time: '2024-03-21' + versions: 3 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 873e6ac4699ed7f6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=873e6ac4699ed7f6 + name: RNAseq_PE (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 249c5d6698c8b98c + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=249c5d6698c8b98c + name: RNAseq_SR (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 44a2b6c8ae54eb31 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=44a2b6c8ae54eb31 + name: ChIPseq_SR (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 45f63151bf4f1a49 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=45f63151bf4f1a49 + name: ATACseq (release v0.10) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f14ebad1c3c20067 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=f14ebad1c3c20067 + name: ATACseq (release v0.11) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1eac2ebffcbb8d59 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1eac2ebffcbb8d59 + name: ChIPseq_PE (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ebbf5cfa946d11d3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ebbf5cfa946d11d3 + name: ChIPseq_PE (release v0.6.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5279af5c95ae4f7a + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5279af5c95ae4f7a + name: CUTandRUN (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e8244d1c80ea0470 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470 + name: Workflow constructed from history 'OGC API Processes Workflow' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - otb_band_math + - otb_mean_shift_smoothing + update_time: '2024-03-20' + versions: 1 +- create_time: '2023-06-27' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Visualisation + - Taxonomic classification + - Box-Whisker plot plotting + - Scatter plot plotting + edam_topic: [] + id: d0ae255151450dad + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=d0ae255151450dad + name: UCB_Soil-Seq_ARGs_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - nanoplot + - taxonomy_krona_chart + - Cut1 + - tp_replace_in_line + - join1 + - mergeCols1 + - kraken2 + - datamash_reverse + - minimap2 + update_time: '2024-03-19' + versions: 4 +- create_time: '2024-03-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Genome assembly + - Sequence composition calculation + - Primer removal + - Aggregation + - Coding region prediction + - Scaffolding + - Genome annotation + - Visualisation + - Sequence trimming + - Transcriptome assembly + - Gene prediction + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: e8eb80ee09159bac + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac + name: Workflow TP 18/03 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - quast + - barrnap + - unicycler + - fasterq_dump + - prokka + - cutadapt + - busco + update_time: '2024-03-16' + versions: 4 +- create_time: '2024-03-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8a248dda0131e8ad + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=8a248dda0131e8ad + name: Workflow constructed from history 'TB analysis' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - collapse_dataset + - tp_cat + - tp_replace_in_line + - interactive_tool_rstudio + - tp_easyjoin_tool + - Grep1 + - tb_variant_filter + - snp_dists + - snp_sites + - bcftools_consensus + update_time: '2024-03-15' + versions: 0 +- create_time: '2023-10-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 011f701c5a55bfdf + latest_version: 128 + license: null + link: https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf + name: Mgnify ML + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + tools: + - interactive_tool_jupyter_notebook + - __BUILD_LIST__ + update_time: '2024-03-15' + versions: 128 +- create_time: '2024-03-14' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Pairwise sequence alignment + edam_topic: [] + id: faf99fbb0fa792b9 + latest_version: 12 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=faf99fbb0fa792b9 + name: smallopttest + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + - pick_value + update_time: '2024-03-15' + versions: 12 +- create_time: '2024-03-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 553a8e0d8b717f9d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=553a8e0d8b717f9d + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: [] + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Matthias Bernt + - UFZ Leipzig + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: b483cf6a138d2372 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b483cf6a138d2372 + name: dada2 amplicon analysis pipeline - for paired en (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:amplicon + tools: + - dada2_makeSequenceTable + - __UNZIP_COLLECTION__ + - dada2_seqCounts + - dada2_assignTaxonomyAddspecies + - dada2_filterAndTrim + - __APPLY_RULES__ + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: c5841e0458a4ebf7 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c5841e0458a4ebf7 + name: Velocyto-on10X-filtered-barcodes (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - velocyto_cli + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 7b710a3f932dffa7 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7b710a3f932dffa7 + name: Velocyto-on10X-from-bun (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - __APPLY_RULES__ + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 33a052f9a3d5551d + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.eu/published/workflow?id=33a052f9a3d5551d + name: Assembly-decontamination-VGP9 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 6b02df749d20cae1 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6b02df749d20cae1 + name: Parallel Accession Down (release v0.1.10) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 0599f049e4697839 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0599f049e4697839 + name: 'COVID-19: variation analysis on WGS SE (release v0.1.5)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2024-03-14' + versions: 1 +- create_time: '2023-09-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0603f0898211f806 + latest_version: 80 + license: null + link: https://usegalaxy.eu/published/workflow?id=0603f0898211f806 + name: Normalization + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + tools: + - map_param_value + - __EXTRACT_DATASET__ + - Grep1 + - __FILTER_EMPTY_DATASETS__ + - __BUILD_LIST__ + update_time: '2024-03-13' + versions: 80 +- create_time: '2024-03-08' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: 309969a261189b5f + latest_version: 36 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=309969a261189b5f + name: TreeValGal_Mar8 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - mashmap + - bedtools_genomecoveragebed + - Add_a_column1 + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - jbrowse2 + - minimap2 + - deeptools_bam_coverage + - fasta_compute_length + update_time: '2024-03-13' + versions: 36 +- create_time: '2024-01-03' + creators: [] + doi: '' + edam_operation: + - Scaffolding + - Transcriptome assembly + - Sequence assembly validation + - Genome assembly + edam_topic: [] + id: 88f80a31e3ff8663 + latest_version: 12 + license: null + link: https://usegalaxy.eu/published/workflow?id=88f80a31e3ff8663 + name: Snail plot using 'BlobToolKit' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - blobtoolkit + - busco + - interactive_tool_blobtoolkit + update_time: '2024-03-12' + versions: 12 +- create_time: '2024-03-12' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Taxonomic classification + - Sequencing quality control + edam_topic: [] + id: 04ed3f21de17aa1d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=04ed3f21de17aa1d + name: Cholera_QC + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - kraken2 + - fastp + - multiqc + update_time: '2024-03-12' + versions: 1 +- create_time: '2024-03-11' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Visualisation + - Taxonomic classification + - Box-Whisker plot plotting + - Scatter plot plotting + edam_topic: [] + id: 14714876dda7186d + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=14714876dda7186d + name: PARE-Seq_ARGs_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - nanoplot + - taxonomy_krona_chart + - Cut1 + - tp_replace_in_line + - join1 + - mergeCols1 + - kraken2 + - datamash_reverse + - minimap2 + update_time: '2024-03-11' + versions: 3 +- create_time: '2024-03-07' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 0d41c30f6952f790 + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=0d41c30f6952f790 + name: Rename collection elements + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + update_time: '2024-03-11' + versions: 7 +- create_time: '2022-04-19' + creators: [] + doi: '' + edam_operation: + - Data handling + - Base-calling + - Genome assembly + - De-novo assembly + - Filtering + - Scaffolding + - Read binning + - Variant calling + - Pairwise sequence alignment + - Transcriptome assembly + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 83a1b8949d87e3da + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da + name: ORG.one_Workflow_v1.0 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - CONVERTER_gz_to_uncompressed + - medaka_consensus_pipeline + - flye + - racon + - gfastats + - filtlong + - minimap2 + - __BUILD_LIST__ + - busco + - purge_dups + update_time: '2024-03-10' + versions: 7 +- create_time: '2023-09-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e2d0d5340975c87f + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=e2d0d5340975c87f + name: BlastN RBH + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_makeblastdb + - ncbi_blastn_wrapper + update_time: '2024-03-09' + versions: 5 +- create_time: '2024-03-07' + creators: + - Leonid Kostrykin + doi: '' + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: 6fbd9b2274c62ebe + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe + name: Segmentation and counting of cell nuclei in fluorescence microscopy images + (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ip_convertimage + - ip_threshold + - ip_overlay_images + - ip_count_objects + - ip_binary_to_labelimage + - ip_filter_standard + - ip_histogram_equalization + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - 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name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: a72e3cb6eb656102 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a72e3cb6eb656102 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 2e6ed783bdf05d16 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=2e6ed783bdf05d16 + name: Scaffolding-BioNano-VGP7 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: f91245e580319e65 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=f91245e580319e65 + name: Purge-duplicate-contigs-VGP6 (release v0.3.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: da41880826c3d758 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=da41880826c3d758 + name: baredSC_2d_logN (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 3410a75a2a4899dc + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3410a75a2a4899dc + name: baredSC_1d_logN (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 587e4d5ce25f48da + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=587e4d5ce25f48da + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 2e6561d8dadc9e17 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2e6561d8dadc9e17 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 2a33d4fcb806e942 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2a33d4fcb806e942 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 7b7d6a5c6c65d74b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b + name: 'COVID-19: consensus construction (release v0.4.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 05bd1d9c61df5d16 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=05bd1d9c61df5d16 + name: 'COVID-19: variation analysis reporting (release v0.3.3)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: fcf745185d6e0ea4 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=fcf745185d6e0ea4 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.5.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-01' + creators: + - Center for Phage Technology, Texas A&M University + - Jason Gill + doi: '' + edam_operation: + - Protein feature detection + - Genome visualisation + - Sequence motif recognition + edam_topic: [] + id: f62d7c0c7cc57eb6 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6 + name: CPT Phage Functional Workflow v2024.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CPT + - phage + - Apollo + tools: + - edu.tamu.cpt.fasta.remove_desc + - ncbi_blastp_wrapper + - blastxml_to_gapped_gff3 + - gff3.rebase + - edu.tamu.cpt.fasta.lipory + - edu.tamu.cpt.gff3.cdsParents + - edu.tamu.cpt.gff3.remove_annots + - interproscan + - edu.tamu.cpt.gff3.require_phage_start + - edu.tamu.cpt.gff3.export_seq + - edu.tamu.cpt.fasta.seq_trans + - fetch_jbrowse + - jbrowse + - iframe + - create_or_update + - get_orfs_or_cdss + update_time: '2024-03-05' + versions: 5 +- create_time: '2024-01-27' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + edam_topic: [] + id: a20e806c2bdba5c1 + latest_version: 15 + license: null + link: https://usegalaxy.eu/published/workflow?id=a20e806c2bdba5c1 + name: make_synteny_paf_TreeValGal_jan27 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + update_time: '2024-03-05' + versions: 15 +- create_time: '2024-03-01' + creators: + - Ross Lazarus + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structure visualisation + - Genome annotation + - Genome visualisation + - Data handling + - Pathway visualisation + - Sequence file editing + - Mapping + edam_topic: [] + id: 1ce406de61de8492 + latest_version: 13 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1ce406de61de8492 + name: TreeValGal_Mar1 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seqtk_telo + - bedtools_makewindowsbed + - windowmasker_mkcounts + - mashmap + - Add_a_column1 + - bedtools_genomecoveragebed + - gfastats + - repeatmasker_wrapper + - windowmasker_ustat + - jbrowse2 + - minimap2 + - fasta_compute_length + update_time: '2024-03-04' + versions: 13 +- create_time: '2024-03-03' + creators: + - Julia Jakiela + - Wendi Bacon + doi: '' + edam_operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + edam_topic: [] + id: e06934a35fc18f2c + latest_version: 9 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c + name: Generating a single cell matrix using Alevin + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - join1 + - dropletutils_read_10x + - sceasy_convert + - _dropletBarcodePlot + - dropletutils_empty_drops + update_time: '2024-03-03' + versions: 9 +- create_time: '2023-04-21' + creators: + - Wendi Bacon + - Julia Jakiela + doi: '' + edam_operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + edam_topic: [] + id: c6adc3b665828a6f + latest_version: 29 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f + name: Generating a single cell matrix using Alevin 1.9 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:transcriptomics + - name:singlecell + - name:training + tools: + - Cut1 + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - join1 + - dropletutils_read_10x + - sceasy_convert + - _dropletBarcodePlot + - dropletutils_empty_drops + update_time: '2024-03-03' + versions: 29 +- create_time: '2024-03-02' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + edam_topic: [] + id: c8deb8952abce1ec + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c8deb8952abce1ec + name: 'Workflow constructed from history ''Tarea 3.1: RNA-seq''' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - clusterprofiler_go + - limma_voom + update_time: '2024-03-02' + versions: 0 +- create_time: '2024-03-01' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: e85c9385870aadcc + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e85c9385870aadcc + name: "Workflow V\xEDctor M. Garc\xEDa Silva 'Tarea 2.1' RNA-seq" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - multiqc + - cshl_fastq_quality_filter + - featurecounts + - hisat2 + update_time: '2024-03-02' + versions: 1 +- create_time: '2024-03-01' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + edam_topic: [] + id: 8ab363878cd34ef0 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=8ab363878cd34ef0 + name: 'Workflow constructed from history ''Taller 3: ARN-Seq Parte 2''' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - clusterprofiler_go + - limma_voom + update_time: '2024-03-01' + versions: 0 +- create_time: '2024-03-01' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + edam_topic: [] + id: 09c77b6fc5add851 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=09c77b6fc5add851 + name: Workflow constructed from history 'Taller 3 RNA-Seq (Parte II)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - 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VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-01-31' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + edam_topic: [] + id: a403c661bf1bc4fa + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=a403c661bf1bc4fa + name: KRAKEN_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_replace_in_line + - kraken2 + - taxonomy_krona_chart + - datamash_reverse + update_time: '2024-02-13' + versions: 4 +- create_time: '2024-02-10' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + - Gene-set enrichment analysis + - Gene functional annotation + edam_topic: [] + id: fa83e26e05418370 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=fa83e26e05418370 + name: "D\xEDa 2 -Tarea 4: Fgsea y Goseg" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fgsea + - Cut1 + - tp_sort_header_tool + - Add_a_column1 + - join1 + - CONVERTER_uncompressed_to_gz + - goseq + - sklearn_numeric_clustering + - limma_voom + update_time: '2024-02-10' + versions: 4 +- create_time: '2024-02-08' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Genome visualisation + - Sequence annotation + - Genetic variation analysis + edam_topic: [] + id: c0f225536e78a178 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=c0f225536e78a178 + name: CPT Phage Structural Workflow v2024.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CPT + - phage + - Apollo + tools: + - edu.tamu.cpt.external.aragorn-gff3 + - edu.tamu.cpt.fasta.remove_desc + - metagene_annotator + - edu.tamu.cpt2.util.mga_to_gff3 + - filter_tabular + - iframe + - edu.tamu.cpt.gff3.cdsParents + - aragorn_trna + - edu.tamu.cpt2.util.glimmer3_to_gff3 + - edu.tamu.cpt.gff3.remove_annots + - edu.tamu.cpt.genbank.shinefind + - glimmer_not_knowledge_based + - 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name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-02-08' + versions: 1 +- create_time: '2024-02-08' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: 4cb8f782994763a4 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4cb8f782994763a4 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-02-08' + versions: 1 +- create_time: '2023-09-07' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Sequence assembly + - Read pre-processing + - Read mapping + - Sequence merging + - Sequencing quality control + edam_topic: [] + id: 4643edf74f3eaec3 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3 + name: Promoter Library Analysis with Barcodes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - flash + - fastp + - Cut1 + - tp_sort_header_tool + - Grouping1 + - tp_easyjoin_tool + - fastq_to_tabular + - cshl_fastx_trimmer + - samtools_view + - bowtie2 + update_time: '2024-02-06' + versions: 6 +- create_time: '2024-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a30d511e3dda0895 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=a30d511e3dda0895 + name: Workflow metadata management EML from a datatable + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - geo_cov_template + - makeeml + - __BUILD_LIST__ + - __MERGE_COLLECTION__ + - taxo_cov_template + - eal_table_template + update_time: '2024-02-04' + versions: 4 +- create_time: '2024-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f98560da584d5abf + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f98560da584d5abf + name: EML to ISO19139 to DCAT - GeoDCAT + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cat1 + - tp_head_tool + - xmlstarlet + - Remove beginning1 + update_time: '2024-02-04' + versions: 1 +- create_time: '2024-02-03' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 6deb9781d9f45a52 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=6deb9781d9f45a52 + name: Workflow constructed from history 'exam 1' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - bowtie2 + update_time: '2024-02-03' + versions: 0 +- create_time: '2024-02-02' + creators: [] + doi: '' + edam_operation: + - Gene-set enrichment analysis + edam_topic: [] + id: 73a9ab4f0f0b9907 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=73a9ab4f0f0b9907 + name: "Workflow constructed from history 'D\xEDa 2 - Tarea extra (RNA-seq) - Javier\ + \ Garc\xEDa Flores/fgseq'" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - fgsea + - Cut1 + update_time: '2024-02-02' + versions: 1 +- create_time: '2024-01-26' + creators: [] + doi: '' + edam_operation: + - Gene functional annotation + edam_topic: [] + id: 032ad839dab7ae70 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=032ad839dab7ae70 + name: "Workflow constructed from history 'D\xEDa 2 - Tarea extra (RNA-seq) - Javier\ + \ Garc\xEDa Flores/goseq'" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Add_a_column1 + - goseq + - join1 + - Cut1 + update_time: '2024-02-02' + versions: 2 +- create_time: '2023-11-15' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Phylogenetic tree reconstruction + - Phylogenetic tree generation + - Phylogenetic tree generation (from molecular sequences) + - Sequence motif recognition + - Phylogenetic tree analysis + - Sequence clustering + - Multiple sequence alignment + - Sequence cluster visualisation + - Sequence visualisation + edam_topic: [] + id: 974cc681d07ec788 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=974cc681d07ec788 + name: BLAST on generated sequences. Clustering on generated sequences (+original), + MSA on clustering output, Phylogenetic tree construction. + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_blastp_wrapper + - rgweblogo3 + - query_tabular + - fasttree + - clustalw + - newick_display + - cd_hit + update_time: '2024-02-02' + versions: 5 +- create_time: '2024-01-31' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Visualisation + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: fba1671d835b6dd3 + latest_version: 0 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=fba1671d835b6dd3 + name: VGP HiFi phased assembly with hifiasm and HiC data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - HiFi_assembly + tools: + - hifiasm + - quast + - Cut1 + - tp_replace_in_line + - merqury + - tp_grep_tool + - cutadapt + - gfa_to_fa + - Convert characters1 + - param_value_from_file + - busco + update_time: '2024-01-31' + versions: 0 +- create_time: '2024-01-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: c58bb47e04157ee6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c58bb47e04157ee6 + name: Velocyto-on10X-filtered-barcodes (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - velocyto_cli + update_time: '2024-01-29' + versions: 1 +- create_time: '2024-01-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: b68b3ceca4a65c58 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b68b3ceca4a65c58 + name: Velocyto-on10X-from-bun (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - __APPLY_RULES__ + update_time: '2024-01-29' + versions: 1 +- create_time: '2024-01-26' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + - Gene-set enrichment analysis + edam_topic: [] + id: 9a83043d5e847318 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=9a83043d5e847318 + name: Workflow 'Taller 2.1 - rnaseq' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - fgsea + - Cut1 + - limma_voom + update_time: '2024-01-27' + versions: 2 +- create_time: '2024-01-26' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Genome visualisation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 5aba0f20d994b1a4 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=5aba0f20d994b1a4 + name: Workflow 'Taller 2 - rnaseq' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - jbrowse + - multiqc + - featurecounts + - hisat2 + update_time: '2024-01-27' + versions: 2 +- create_time: '2024-01-27' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 99c7ec2841af3a20 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=99c7ec2841af3a20 + name: Workflow 'Taller 1 - Chr22' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2024-01-27' + versions: 1 +- create_time: '2024-01-24' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: a8d814a6d86e9661 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661 + name: Workflow 'Taller 1 - control de calidad' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + - fastqe + update_time: '2024-01-27' + versions: 2 +- create_time: '2024-01-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Phylogenetic analysis + - Sequence alignment analysis + - Phylogenetic inference + - Primer removal + - Species frequency estimation + - Sequence similarity search + - Sequencing quality control + - Taxonomic classification + - Sequence composition calculation + - Sequence comparison + - Phylogenetic tree visualisation + - Validation + - Sequence trimming + - Visualisation + - Conversion + - Phylogenetic tree analysis + - Read pre-processing + - Nucleic acid sequence analysis + - Phylogenetic tree editing + edam_topic: [] + id: fdca6c9d394986bf + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf + name: Workflow constructed from history 'metatranscriptomics and rna seq' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - humann_split_stratified_table + - taxonomy_krona_chart + - Cut1 + - export2graphlan + - graphlan + - fastq_paired_end_interlacer + - cutadapt + - metaphlan + - Grep1 + - tp_find_and_replace + - humann_renorm_table + - multiqc + - bg_sortmerna + - humann_unpack_pathways + - humann_rename_table + - graphlan_annotate + - humann_regroup_table + update_time: '2024-01-25' + versions: 0 +- create_time: '2023-10-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 22454322d370b3ff + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=22454322d370b3ff + name: Pipeline chiamata di varianti + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:dnaseq + - name:tutorial + - name:variantcalling + tools: + - fastqc + - bwa_mem2 + - trimmomatic + - vcffilter2 + - samtools_flagstat + - picard_MarkDuplicates + - bcftools_call + - bcftools_mpileup + update_time: '2024-01-25' + versions: 4 +- create_time: '2024-01-25' + creators: + - "B\xE9r\xE9nice Batut" + - Pierre Marin + doi: '' + edam_operation: + - Protein feature detection + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Antimicrobial resistance prediction + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: 3f5fe28793ed0c6c + latest_version: 3 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c + name: Bacterial genome annotation (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - genome-annotation + tools: + - abricate + - bakta + - plasmidfinder + - isescan + - integron_finder + update_time: '2024-01-25' + versions: 3 +- create_time: '2024-01-24' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 055eae88be2d4dd7 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7 + name: "Workflow constructed from history 'D\xEDa 1 - Tarea 1 - Javier Garc\xEDa\ + \ Flores'" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + - fastqe + update_time: '2024-01-24' + versions: 1 +- create_time: '2024-01-18' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: b211fceaecf41c9e + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=b211fceaecf41c9e + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 5115299e77df8104 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=5115299e77df8104 + name: Assembly-Hifi-only-VGP3 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5c15f251642bfa1f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4b4bfc79205d83f1 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4b4bfc79205d83f1 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.5.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 6be946c7ec91835e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6be946c7ec91835e + name: 'COVID-19: variation analysis on WGS SE (release v0.1.4)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ddb21f7793eff83d + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=ddb21f7793eff83d + name: Copernicus tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:climate + tools: + - c3s + update_time: '2024-01-16' + versions: 3 +- create_time: '2023-11-22' + creators: + - khaled Jumah + - Katarzyna Kamieniecka + - Wolfgang Maier + - Krzysztof Poterlowicz + - poterlowicz-lab + doi: '' + edam_operation: + - Statistical calculation + - Genome alignment + - Sequence composition calculation + - Genome indexing + - Read mapping + - Variant calling + - Validation + - Copy number estimation + - Generation + - Sequencing quality control + - Sequence alignment + - Sequence visualisation + edam_topic: [] + id: 75e88603745e069e + latest_version: 18 + license: AGPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=75e88603745e069e + name: Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC + number_of_steps: null + source: https://usegalaxy.eu + tags: + - hCNV + - variant-analysis + - MIRACUM + tools: + - fastqc + - control_freec + - tp_text_file_with_recurring_lines + - trimmomatic + - samtools_calmd + - samtools_view + - __EXTRACT_DATASET__ + - tp_replace_in_line + - samtools_rmdup + - __RELABEL_FROM_FILE__ + - Grep1 + - bamleftalign + - multiqc + - 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chembl + - openbabel_svg_depiction + - ctb_im_rxn_maker + - openbabel_compound_convert + - ctb_silicos_qed + update_time: '2024-01-01' + versions: 7 +- create_time: '2023-10-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 48fe9c4de045d414 + latest_version: 27 + license: null + link: https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414 + name: BasilioAguirreGarcia Pipeline + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - tp_uniq_tool + - trim_galore + - fasterq_dump + - salmon + - __RELABEL_FROM_FILE__ + - tp_tail_tool + - Grep1 + - limma_voom + - gprofiler_gost + - tp_find_and_replace + - regex1 + - Filter1 + update_time: '2023-12-29' + versions: 27 +- create_time: '2023-12-28' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: 90a32c95b60f5221 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=90a32c95b60f5221 + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2023-12-28' + versions: 1 +- create_time: '2023-12-28' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: 865715636d40b798 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=865715636d40b798 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2023-12-28' + versions: 1 +- create_time: '2023-10-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1590085d315aa80e + latest_version: 39 + license: null + link: https://usegalaxy.eu/published/workflow?id=1590085d315aa80e + name: PabloRodriguez_RNASeq + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - tp_uniq_tool + - trim_galore + - fasterq_dump + - salmon + - __RELABEL_FROM_FILE__ + - tp_tail_tool + - Grep1 + - limma_voom + - gprofiler_gost + - tp_find_and_replace + - regex1 + - Filter1 + update_time: '2023-12-26' + versions: 39 +- create_time: '2023-12-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a62f21701ff37788 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a62f21701ff37788 + name: BE480_NGS AnhLe + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bwa + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2023-12-23' + versions: 1 +- create_time: '2023-10-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8bc1c3b9e665ea37 + latest_version: 28 + license: null + link: https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37 + name: "BeatrizLe\xF3nGarc\xEDa_RNASeq" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - tp_uniq_tool + - trim_galore + - fasterq_dump + - salmon + - __RELABEL_FROM_FILE__ + - tp_tail_tool + - Grep1 + - limma_voom + - gprofiler_gost + - tp_find_and_replace + - regex1 + - Filter1 + update_time: '2023-12-22' + versions: 28 +- create_time: '2022-12-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f27abf3c623d3062 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f27abf3c623d3062 + name: scRNASeq 'PBMCs' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_find_cluster + - scanpy_scale_data + - scanpy_read_10x + - scanpy_compute_graph + - scanpy_find_markers + - ucsc_cell_browser + - scanpy_normalise_data + - scanpy_filter_cells + - scanpy_run_umap + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2023-12-19' + versions: 1 +- create_time: '2023-06-09' + creators: + - Wendi Bacon + - Julia Jakiela + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 715ca378c1d68de3 + latest_version: 6 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=715ca378c1d68de3 + name: Filter, Plot and Explore Single-cell RNA-seq Data updated + number_of_steps: null + source: https://usegalaxy.eu + tags: + - transcriptomics + tools: + - anndata_manipulate + - scanpy_find_cluster + - scanpy_scale_data + - anndata_inspect + - scanpy_compute_graph + - scanpy_find_markers + - scanpy_plot_embed + - Cut1 + - scanpy_normalise_data + - join1 + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_plot + - anndata_ops + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2023-12-18' + versions: 6 +- create_time: '2023-12-12' + creators: + - Julia Jakiela + - Morgan Howells + doi: '' + edam_operation: + - Community profiling + - Loading + edam_topic: [] + id: 704e6c9bc51db49f + latest_version: 7 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=704e6c9bc51db49f + name: AnnData to Seurat conversion + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seurat_read10x + - datamash_transpose + - dropletutils + - anndata_inspect + update_time: '2023-12-15' + versions: 7 +- create_time: '2023-12-12' + creators: + - Julia Jakiela + - Morgan Howells + doi: '' + edam_operation: + - Community profiling + - Loading + edam_topic: [] + id: 49a6ddcba35bf085 + latest_version: 7 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=49a6ddcba35bf085 + name: AnnData to SingleCellExperiment (SCE) conversion + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - dropletutils_read_10x + - datamash_transpose + - dropletutils + - anndata_inspect + update_time: '2023-12-15' + versions: 7 +- create_time: '2023-12-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2a13eb981d6ee36e + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=2a13eb981d6ee36e + name: Workflow constructed from history 'BE480 NGS assignment' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-12-14' + versions: 4 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Target-Decoy + - de Novo sequencing + - Tag-based peptide identification + - Expression analysis + - Protein identification + edam_topic: [] + id: 7cfbf4b7bd3f30d3 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3 + name: WF1_Database_Generation_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:clinicalMP + - name:microGalaxy + tools: + - metanovo + - fasta_merge_files_and_filter_unique_sequences + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Heat map generation + - Filtering + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: 8af41219411062ad + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8af41219411062ad + name: WF2_Discovery-Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:clinicalMP + tools: + - ident_params + - maxquant + - fasta_cli + - filter_tabular + - Cut1 + - Remove beginning1 + - tp_cat + - query_tabular + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - Grep1 + - search_gui + - peptide_shaker + - dbbuilder + - msconvert + - Filter1 + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d87fc6685e47d27d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d + name: WF3_VERIFICATION_WORKFLOW + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:clinicalMP + tools: + - pepquery2 + - Remove beginning1 + - Cut1 + - collapse_dataset + - tp_cat + - query_tabular + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - uniprotxml_downloader + - dbbuilder + - Filter1 + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: a49275eb8b2b2ecb + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb + name: WF4_Quantitation_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:clinicalMP + - name:microGalaxy + tools: + - Grouping1 + - Grep1 + - maxquant + - Cut1 + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 755ede37d94dc456 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=755ede37d94dc456 + name: WF5_Data_Interpretation_Worklow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:clinicalMP + tools: + - msstatstmt + - Grep1 + - unipept + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Statistical calculation + - Formatting + - Sequence profile generation + - Format validation + - Sequence motif recognition + - Primer removal + - Coding region prediction + - Data retrieval + - Sequence assembly + - Sequence assembly validation + - Sequencing quality control + - Protein feature detection + - Taxonomic classification + - Gene functional annotation + - Local alignment + - Sequence composition calculation + - Database search + - Validation + - Sequence analysis + - Visualisation + - Sequence trimming + - Conversion + - Probabilistic sequence generation + - Gene prediction + - Sequence generation + - Multiple sequence alignment + - Read pre-processing + edam_topic: [] + id: d57d41e306241396 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=d57d41e306241396 + name: MetaG_extended + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microgalaxy + tools: + - fastqc + - sort1 + - quast + - kofamscan + - fasplit + - tp_cat + - trim_galore + - hmmer_hmmscan + - checkm_lineage_wf + - tp_grep_tool + - tp_awk_tool + - fraggenescan + - coverm_contig + - interproscan + - cat_bins + - maxbin2 + - coverm_genome + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: 01ac8bf9832789e2 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=01ac8bf9832789e2 + name: MetaP + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microgalaxy + tools: + - maxquant + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence alignment analysis + - Gene expression profiling + - Sequence composition calculation + - Sequence comparison + - Primer removal + - Sequence trimming + - Read pre-processing + - Sequence similarity search + - Sequencing quality control + edam_topic: [] + id: 3733bcdf5b458be7 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=3733bcdf5b458be7 + name: MetaT + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microgalaxy + tools: + - fastqc + - collection_column_join + - __UNZIP_COLLECTION__ + - trim_galore + - kallisto_quant + - bg_sortmerna + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Query and retrieval + - Statistical inference + - Quantification + - Filtering + - Indexing + - 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proteomics + - name:microGalaxy + tools: + - metaquantome_stat + - metaquantome_viz + - metaquantome_sample + - metaquantome_expand + - metaquantome_filter + - metaquantome_db + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 68967c922de149ae + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=68967c922de149ae + name: Metaproteomics_GTN + number_of_steps: null + source: https://usegalaxy.eu + tags: + - proteomics + - name:microGalaxy + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Mapping + - Read mapping + - Sequence alignment + edam_topic: [] + id: 0e492839192d26e0 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 + name: Ecoli Comparison + number_of_steps: null + source: https://usegalaxy.eu + tags: + - assembly + - name:microGalaxy + tools: + - collapse_dataset + - join1 + - fasta_compute_length + - tp_sort_header_tool + - datamash_ops + - random_lines1 + - mergeCols1 + - tp_grep_tool + - cat1 + - Grep1 + - tp_cat + - tp_sed_tool + - addValue + - lastz_wrapper_2 + - Filter1 + - fasta_filter_by_length + - Cut1 + - bedtools_complementbed + - bedtools_sortbed + - bedtools_intersectbed + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Statistical calculation + - Visualisation + - Taxonomic classification + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 08eb5e55109c4d9c + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c + name: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - name:microGalaxy + tools: + - fastqc + - fastp + - taxonomy_krona_chart + - Remove beginning1 + - tp_replace_in_line + - kraken2 + - porechop + - datamash_reverse + - multiqc + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: + - "B\xE9r\xE9nice Batut" + - Pratik Jagtap + - Subina Mehta + - Ray Sajulga + - Emma Leith + - Praveen Kumar + - Saskia Hiltemann + - Paul Zierep + doi: '' + edam_operation: [] + edam_topic: [] + id: 7a08ecdf23e0c7a3 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3 + name: Main Metatranscriptomics Analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + tools: [] + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Aggregation + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Mapping assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: 44e53ea319e07daa + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa + name: Copy Of GTN Training - Antibiotic Resistance Detection + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - name:microGalaxy + tools: + - nanoplot + - staramr_search + - PlasFlow + - racon + - unicycler + - miniasm + - gfa_to_fa + - minimap2 + - bandage_image + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: + - "B\xE9r\xE9nice Batut" + - "Teresa M\xFCller" + - Polina Polunina + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Visualisation + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Sequencing quality control + edam_topic: [] + id: 0590554db9794d13 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0590554db9794d13 + name: Identification of the micro-organisms in a beer using Nanopore sequencing + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Metagenomics + - name:microGalaxy + tools: + - fastqc + - fastp + - taxonomy_krona_chart + - krakentools_kreport2krona + - kraken2 + - porechop + - Filter1 + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome assembly + - Sequence composition calculation + - Read mapping + - Primer removal + - Variant calling + - Sequence contamination filtering + - Sequence trimming + - Sequence file editing + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ce5c16ac23c4fbb1 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 + name: workflow-generate-dataset-for-assembly-tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + tools: + - fastqc + - filter_tabular + - tp_cat + - ngsutils_bam_filter + - random_lines1 + - cutadapt + - megahit + - seqtk_subseq + - bowtie2 + - bamtools + - bg_uniq + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Genome assembly + - Sequence assembly visualisation + - Read mapping + - Sequence assembly validation + edam_topic: [] + id: 62c47e3c9d4f3aa3 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 + name: Metagenomics assembly tutorial workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + tools: + - collection_column_join + - quast + - bandage_info + - megahit_contig2fastg + - metaspades + - megahit + - bandage_image + - bowtie2 + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: c2b7ec5aacfc6107 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 + name: WGS Part In "Analyses Of Metagenomics Data - The Global Picture" + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - name:microGalaxy + tools: + - metaphlan2krona + - taxonomy_krona_chart + - humann2_renorm_table + - humann2 + - metaphlan2 + - humann2_regroup_table + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Statistical calculation + - Visualisation + - Taxonomic classification + - Phylogenetic tree analysis + - Nucleic acid sequence analysis + - Aggregation + edam_topic: [] + id: 4f0daf8e9dd54127 + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 + name: Taxonomic Profiling and Visualization of Metagenomic Data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Metagenomics + - name:microGalaxy + tools: + - __UNZIP_COLLECTION__ + - taxonomy_krona_chart + - krakentools_kreport2krona + - est_abundance + - kraken2 + - interactive_tool_phinch + - kraken_biom + - interactive_tool_pavian + - metaphlan + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 565c989730f68362 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=565c989730f68362 + name: Amplicon Tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - name:microGalaxy + tools: + - mothur_summary_seqs + - mothur_make_group + - mothur_filter_seqs + - krona-text + - mothur_screen_seqs + - mothur_count_seqs + - mothur_cluster_split + - mothur_make_biom + - mothur_merge_files + - mothur_make_shared + - mothur_unique_seqs + - mothur_align_seqs + - mothur_classify_otu + - mothur_classify_seqs + - mothur_pre_cluster + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Genome visualisation + - Variant calling + - Phylogenetic tree generation + edam_topic: [] + id: 515ef1601bc24a6c + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c + name: Microbial Variant Calling + number_of_steps: null + source: https://usegalaxy.eu + tags: + - variant-analysis + - name:microGalaxy + tools: + - jbrowse + - snippy + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 291c36e1b18e9deb + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb + name: Calling variants in non-diploid systems + number_of_steps: null + source: https://usegalaxy.eu + tags: + - variant-analysis + - name:microGalaxy + tools: + - fastqc + - picard_MergeSamFiles + - Cut1 + - bamFilter + - vcffilter2 + - vcf2tsv + - bamleftalign + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: c67d2e75eeb4fd19 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 + name: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - name:microGalaxy + tools: + - mothur_heatmap_sim + - mothur_make_biom + - mothur_cluster + - mothur_rarefaction_single + - mothur_align_seqs + - mothur_classify_seqs + - mothur_venn + - taxonomy_krona_chart + - mothur_get_groups + - mothur_seq_error + - mothur_make_shared + - newick_display + - mothur_remove_groups + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_dist_shared + - mothur_dist_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_tree_shared + - mothur_unique_seqs + - mothur_classify_otu + - mothur_taxonomy_to_krona + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - XY_Plot_1 + - mothur_count_groups + - mothur_cluster_split + - mothur_sub_sample + - mothur_pre_cluster + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Multiple sequence alignment + - Sequence alignment analysis + - Phylogenetic tree generation + edam_topic: [] + id: 86900be4282d4b1d + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d + name: Comparative gene analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - vgp + - genome-annotation + - name:microGalaxy + tools: + - tp_split_on_column + - Cut1 + - collapse_dataset + - Add_a_column1 + - rbc_mafft + - join1 + - regexColumn1 + - gops_intersect_1 + - cat1 + - tab2fasta + - bg_diamond + - bg_diamond_view + - rapidnj + - Filter1 + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Aggregation + - Coding region prediction + - Validation + - Genome annotation + - Visualisation + - Gene prediction + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 8f3ce55d44d9f369 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369 + name: Unicycler training + number_of_steps: null + source: https://usegalaxy.eu + tags: + - assembly + - name:microGalaxy + tools: + - fastqc + - quast + - unicycler + - prokka + - multiqc + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: 3c233cc56d4df8b0 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 + name: Apollo Load Test + number_of_steps: null + source: https://usegalaxy.eu + tags: + - genome-annotation + - name:microGalaxy + tools: + - list_organism + - create_account + - jbrowse + - iframe + - create_or_update + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Gene prediction + - Genome annotation + - Genome visualisation + - Coding region prediction + edam_topic: [] + id: e1894c36f1ab4ab4 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 + name: Genome Annotation with Prokka [Feb 2020] + number_of_steps: null + source: https://usegalaxy.eu + tags: + - genome-annotation + - name:microGalaxy + tools: + - prokka + - jbrowse + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Base-calling + - Genome assembly + - De-novo assembly + - Coding region prediction + - Pairwise sequence alignment + - Variant calling + - Sequence analysis + - Genome annotation + - Scatter plot plotting + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Gene prediction + - Sequence assembly + - Sequence assembly visualisation + - Sequence visualisation + edam_topic: [] + id: 152223c8aed27357 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=152223c8aed27357 + name: Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - wmdi + - name:microGalaxy + tools: + - tp_text_file_with_recurring_lines + - trimmomatic + - fasta2tab + - join1 + - deeptools_bam_coverage + - fasta_compute_length + - staramr_search + - tbl2gff3 + - tp_sort_header_tool + - PlasFlow + - circos_gc_skew + - Grep1 + - tp_split_on_column + - nanoplot + - circos_interval_to_tile + - tp_cat + - Add_a_column1 + - regex_replace + - circos_wiggle_to_scatter + - tp_cut_tool + - prokka + - tp_head_tool + - gff2bed1 + - minimap2 + - circos + - Filter1 + - medaka_consensus_pipeline + - Cut1 + - flye + - bg_column_arrange_by_header + - tp_easyjoin_tool + - tab2fasta + - jbrowse + - ncbi_blastn_wrapper + - bandage_image + - regex1 + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Phylogenetic tree analysis + edam_topic: [] + id: 875b3ca170ac12a1 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 + name: Mtb phylogeny + number_of_steps: null + source: https://usegalaxy.eu + tags: + - evolution + - name:microGalaxy + tools: + - raxml + - interactive_tool_rstudio + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6d333ed886aab471 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 + name: From VCFs to SNP distance matrix + number_of_steps: null + source: https://usegalaxy.eu + tags: + - evolution + - name:microGalaxy + tools: + - tp_cat + - tb_variant_filter + - snp_dists + - snp_sites + - bcftools_consensus + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Variant calling + - Phylogenetic tree generation + edam_topic: [] + id: 3a8fde248a4d0383 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 + name: From Fastqs to VCFs and BAMs + number_of_steps: null + source: https://usegalaxy.eu + tags: + - evolution + - name:microGalaxy + tools: + - __MERGE_COLLECTION__ + - trimmomatic + - snippy + - tb_variant_filter + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: [] + doi: '' + edam_operation: + - Antimicrobial resistance prediction + edam_topic: [] + id: d0d6dae0d1eecc21 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 + name: From BAMs to drug resistance prediction with TB-profiler + number_of_steps: null + source: https://usegalaxy.eu + tags: + - evolution + - name:microGalaxy + tools: + - addName + - tp_cat + - tp_replace_in_line + - tp_sed_tool + - tp_grep_tool + - samtools_view + - __MERGE_COLLECTION__ + - tb_profiler_profile + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Taxonomic classification + - Phylogenetic tree generation + - Sequence composition calculation + - Phylogenetic tree visualisation + - Variant calling + - Validation + - Antimicrobial resistance prediction + - Sequencing quality control + edam_topic: [] + id: 3ff4dbcc7a602e6b + latest_version: 0 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b + name: M. tuberculosis Variant Analysis tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: + - variant-analysis + - prokaryote + - name:microGalaxy + tools: + - fastqc + - trimmomatic + - snippy + - tbvcfreport + - kraken2 + - jbrowse + - tb_variant_filter + - multiqc + - tb_profiler_profile + update_time: '2023-12-14' + versions: 0 +- create_time: '2023-12-14' + creators: + - Julia Jakiela + doi: '' + edam_operation: [] + edam_topic: [] + id: 0909859a02040efc + latest_version: 6 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=0909859a02040efc + name: EBI SCXA to AnnData (Scanpy) or Seurat Object + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_read_10x + - seurat_read10x + - regexColumn1 + - tp_grep_tool + - tp_find_and_replace + - anndata_ops + - retrieve_scxa + update_time: '2023-12-14' + versions: 6 +- create_time: '2023-12-13' + creators: + - Julia Jakiela + doi: '' + edam_operation: [] + edam_topic: [] + id: 35c092316cdc27d1 + latest_version: 7 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=35c092316cdc27d1 + name: AnnData to Cell Data Set (CDS) conversion + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - datamash_transpose + - monocle3_create + - anndata_inspect + update_time: '2023-12-14' + versions: 7 +- create_time: '2023-12-13' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: 21a39ac4c1becb31 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 + name: Compute Allel Frequency Table from paired reads + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - HPylori + tools: + - snpSift_filter + - bcftools_view + - vcf2tsv + - bcftools_norm + - tp_awk_tool + - bowtie2 + - freebayes + update_time: '2023-12-13' + versions: 2 +- create_time: '2023-10-27' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: 61fe08fb3d5e83f8 + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 + name: Reference genome choice (indels, coverage, depth) for short reads + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - HPylori + tools: + - collection_element_identifiers + - collapse_dataset + - tp_cat + - samtools_coverage + - vcf2tsv + - bcftools_norm + - samtools_depth + - bowtie2 + - freebayes + update_time: '2023-12-13' + versions: 13 +- create_time: '2023-12-12' + creators: [] + doi: '' + edam_operation: + - Formatting + - Visualisation + - k-mer counting + - Nucleic acid feature detection + - Comparison + - Alignment + - Mapping + edam_topic: [] + id: 437704898229dfb6 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=437704898229dfb6 + name: MGnify amplicon rRNA-prediction + ITS + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MGnify_Amplicon_Showcase + - name:microGalaxy + tools: + - cmsearch_deoverlap + - gops_concat_1 + - taxonomy_krona_chart + - query_tabular + - biom_convert + - bedtools_maskfastabed + - tp_awk_tool + - bedtools_getfastabed + - infernal_cmsearch + - mapseq + update_time: '2023-12-13' + versions: 1 +- create_time: '2023-12-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Sequence merging + - Validation + - Sequence contamination filtering + - Sequence trimming + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8f415b0c409f56f7 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 + name: MGnify amplicon QC + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MGnify_Amplicon_Showcase + - name:microGalaxy + tools: + - fastqc + - fastp + - trimmomatic + - __UNZIP_COLLECTION__ + - cshl_fasta_formatter + - fastq_to_fasta_python + - prinseq + - fastq_dump + - tp_find_and_replace + - iuc_pear + - multiqc + update_time: '2023-12-13' + versions: 1 +- create_time: '2022-09-02' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: cd3398e29f375d97 + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=cd3398e29f375d97 + name: '1-Identify variants saxy ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - trimmomatic + - mimodd_vcf_filter + - jvarkit_wgscoverageplotter + - mimodd_varcall + - cat1 + - snpEff + - mimodd_varreport + - mimodd_varextract + - bowtie2 + update_time: '2023-12-12' + versions: 11 +- create_time: '2023-12-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Data handling + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: ccef778cfd9024d1 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1 + name: RNA-seq (Drosophila melanogaster) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - deg_annotate + - join1 + - __TAG_FROM_FILE__ + - featurecounts + - collection_element_identifiers + - tp_sort_header_tool + - ggplot2_heatmap2 + - cutadapt + - __FLATTEN__ + - rseqc_infer_experiment + - rna_star + - multiqc + - deseq2 + - gtftobed12 + - tp_replace_in_line + - tp_cat + - Filter1 + - Cut1 + update_time: '2023-12-09' + versions: 0 +- create_time: '2023-06-07' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + - RNA-Seq quantification + - Genome indexing + - Mapping + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + - Differential gene expression analysis + - Peak calling + - Generation + - Read summarisation + edam_topic: [] + id: 0229f3f3835c2d53 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=0229f3f3835c2d53 + name: Exercise2CB + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - collection_column_join + - trimmomatic + - __EXTRACT_DATASET__ + - bedtools_intersectbed + - tp_awk_tool + - edger + - macs2_callpeak + - rna_star + - __BUILD_LIST__ + - comp1 + - featurecounts + - bwa_mem + update_time: '2023-12-08' + versions: 6 +- create_time: '2021-11-10' + creators: [] + doi: '' + edam_operation: + - Validation + - RNA-Seq quantification + - Read mapping + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 4566262dd0acc8ab + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab + name: ' Cloud-Aerosole MT-MG Functional Profiling' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - metatranscriptomics + - name:microGalaxy + tools: + - multiqc + - bowtie2 + - featurecounts + update_time: '2023-12-07' + versions: 2 +- create_time: '2021-11-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Fold recognition + - Sequence alignment analysis + - Information extraction + - Query and retrieval + - Read mapping + - Genome annotation + - Sequence clustering + - Sequence assembly validation + - Sequencing quality control + - Gene functional annotation + - Genome assembly + - Sequence composition calculation + - Mapping + - Sequence annotation + - Homology-based gene prediction + - Validation + - Sequence analysis + - Visualisation + edam_topic: [] + id: 9b9e1e28f3683f92 + latest_version: 72 + license: null + link: https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 + name: Cloud-Aerosole MT-MG Reference Gene Catalog Building + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - metatranscriptomics + - name:microGalaxy + tools: + - fastqc + - quast + - metagene_annotator + - kofamscan + - metaeuk_easy_predict + - cat1 + - eggnog_mapper + - translate_nucleotides + - bg_diamond_makedb + - megahit + - bedtools_getfastabed + - multiqc + - cd_hit + - dbbuilder + - bowtie2 + - bg_diamond + update_time: '2023-12-07' + versions: 72 +- create_time: '2021-11-01' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: bb604ff5e010e7ab + latest_version: 51 + license: null + link: https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab + name: Cloud-Aerosole MT-MG Pre-Processing + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - metatranscriptomics + - name:microGalaxy + tools: + - fastqc + - multiqc + - trimmomatic + update_time: '2023-12-07' + versions: 51 +- create_time: '2022-06-29' + creators: [] + doi: '' + edam_operation: + - Expression analysis + - Read mapping + - Taxonomic classification + - Cross-assembly + edam_topic: [] + id: bdc7cfaac0db2eab + latest_version: 28 + license: null + link: https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab + name: Cloud Aerosol MT-MG Contamination Filtering + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - metatranscriptomics + - name:microGalaxy + tools: + - seq_filter_by_id + - filter_tabular + - recentrifuge + - kraken2 + - fastq_to_tabular + - bowtie2 + update_time: '2023-12-07' + versions: 28 +- create_time: '2022-09-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Visualisation + - Taxonomic classification + - Cross-assembly + - Expression analysis + - Filtering + - Standardisation and normalisation + edam_topic: [] + id: e69b555faa6bb962 + latest_version: 18 + license: null + link: https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 + name: Cloud-Aerosole MT-MG Taxonomic Profiling + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + - metatranscriptomics + - name:microGalaxy + tools: + - maaslin2 + - recentrifuge + - kraken2 + - interactive_tool_phinch + - kraken_biom + update_time: '2023-12-07' + versions: 18 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 4025b5dca188e6a4 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4025b5dca188e6a4 + name: baredSC_2d_logN (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 4eb8aec8a5be98b3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4eb8aec8a5be98b3 + name: baredSC_1d_logN (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: ea8bb8eefdb4ba7a + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ea8bb8eefdb4ba7a + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 9e4df2893767591a + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9e4df2893767591a + name: Get Confident Peaks From ChIP_PE duplicates (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 55a9fc5d30392777 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=55a9fc5d30392777 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-10-01' + creators: + - Julia Jakiela + - Wendi Bacon + doi: '' + edam_operation: [] + edam_topic: [] + id: acb9131e84de1ae0 + latest_version: 7 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=acb9131e84de1ae0 + name: How to downsample FASTQ files + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_tail_tool + - fastq_to_tabular + - tabular_to_fastq + update_time: '2023-12-03' + versions: 7 +- create_time: '2021-09-02' + creators: + - Bradley W. Langhorst + - New England Biolabs + doi: '' + edam_operation: [] + edam_topic: [] + id: 3f8e91403a27f1c1 + latest_version: 28 + license: AGPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=3f8e91403a27f1c1 + name: Merge Lanes by Sample + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_cat + - __FLATTEN__ + - __ZIP_COLLECTION__ + - __APPLY_RULES__ + update_time: '2023-12-03' + versions: 28 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: c9f83ce86d407902 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c9f83ce86d407902 + name: Generic variation analysis reporting (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - mpvx + - generic + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - compose_text_param + - tp_find_and_replace + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 3dec7c9b02c3d1ee + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.eu/published/workflow?id=3dec7c9b02c3d1ee + name: Assembly-decontamination-VGP9 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 12a018217ee146ca + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.eu/published/workflow?id=12a018217ee146ca + name: Assembly-decontamination-VGP9 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 9f2d18f0d0896e8b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=9f2d18f0d0896e8b + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: 471eb8b4c54f897d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=471eb8b4c54f897d + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: a85be448600a6789 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=a85be448600a6789 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: db6640887b5ca0cd + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=db6640887b5ca0cd + name: kmer-profiling-hifi-VGP1 (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 700fa3ab11a8f3e2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=700fa3ab11a8f3e2 + name: Purge-duplicate-contigs-VGP6 (release v0.3.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: a37d1e0db16cfb67 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=a37d1e0db16cfb67 + name: Scaffolding-HiC-VGP8 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: bc87309a8763d0b4 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=bc87309a8763d0b4 + name: Assembly-Hifi-only-VGP3 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: ae16643c04ad1216 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ae16643c04ad1216 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 8f9dc5ba61a02815 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=8f9dc5ba61a02815 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 7582a48054c44d6e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7582a48054c44d6e + name: Get Confident Peaks From ChIP_SR duplicates (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d768c0e0df4d432e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d768c0e0df4d432e + name: CUTandRUN (release v0.6.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 614807d57979554c + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=614807d57979554c + name: Generic variation analysis on WGS PE (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - mpxv + - generic + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 5d793801998146bc + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5d793801998146bc + name: Create GRO and TOP complex files (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ambertools_acpype + - Cut1 + - ctb_rdkit_descriptors + - gmx_setup + - tp_grep_tool + - gmx_merge_topology_files + - param_value_from_file + - ambertools_antechamber + - openbabel_compound_convert + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 07e1478df88a17cc + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc + name: MMGBSA calculations with GROMACS (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 3c6ff60d1d3ceb3d + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d + name: MMGBSA calculations with GROMACS (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: d1357759d0962144 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d1357759d0962144 + name: dcTMD calculations with GROMACS (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_text_file_with_recurring_lines + - split_file_to_collection + - add_line_to_file + - tp_cat + - gmx_sim + - biomd_neqgamma + - gmx_solvate + - tp_sed_tool + - gmx_makendx + - compose_text_param + - ctb_online_data_fetch + - param_value_from_file + - gmx_em + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 8a1ddbae2d1c3f12 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=8a1ddbae2d1c3f12 + name: Parallel Accession Down (release v0.1.9) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 5ded4002e684a02c + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c + name: 'COVID-19: consensus construction (release v0.4.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 036990ecf300a99f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=036990ecf300a99f + name: 'COVID-19: variation analysis reporting (release v0.3.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 429ae28a178cd07c + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=429ae28a178cd07c + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.3.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a9e1a6b90dbd2518 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a9e1a6b90dbd2518 + name: 'COVID-19: variation analysis on WGS PE (release v0.2.4)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-24' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 3a4ef58e24e7b1ef + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=3a4ef58e24e7b1ef + name: Find with the highest number of features + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2023-11-24' + versions: 1 +- create_time: '2023-11-03' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Structural variation detection + - Sequence analysis + edam_topic: [] + id: 35a9136ddf37d589 + latest_version: 15 + license: null + link: https://usegalaxy.eu/published/workflow?id=35a9136ddf37d589 + name: nanopore variants analysis_ SVA detection + number_of_steps: null + source: https://usegalaxy.eu + tags: + - structuralvariantnanopore + - nanopore + tools: + - samtools_calmd + - sniffles + - samtools_sort + - samtools_stats + - minimap2 + update_time: '2023-11-23' + versions: 15 +- create_time: '2023-11-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8a81615501be20fd + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8a81615501be20fd + name: Metadata conversion from one standard to another + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - xmlstarlet + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 1f2a1438e41188f2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=1f2a1438e41188f2 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 238606356787b876 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=238606356787b876 + name: kmer-profiling-hifi-VGP1 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: d261bbd05889ce75 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=d261bbd05889ce75 + name: Purge-duplicate-contigs-VGP6 (release v0.3.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: b287bb779cf686ef + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=b287bb779cf686ef + name: Scaffolding-HiC-VGP8 (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: bb1680ec6dde6004 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=bb1680ec6dde6004 + name: Parallel Accession Down (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: ad2c1d14c0d2dd2f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ad2c1d14c0d2dd2f + name: Parallel Accession Down (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-10' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Structural variation detection + - Sequence analysis + - Pairwise sequence alignment + edam_topic: [] + id: cb54883452a73019 + latest_version: 17 + license: null + link: https://usegalaxy.eu/published/workflow?id=cb54883452a73019 + name: nanopore variants phasing methylation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - phasing + - nanopore + tools: + - clair3 + - samtools_calmd + - sniffles + - samtools_sort + - samtools_stats + - minimap2 + update_time: '2023-11-21' + versions: 17 +- create_time: '2023-11-21' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 475e4a5c3b1acda3 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=475e4a5c3b1acda3 + name: find exon with the highest number of features + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2023-11-21' + versions: 2 +- create_time: '2023-11-21' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: e71a3c5ca3c31df1 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=e71a3c5ca3c31df1 + name: find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2023-11-21' + versions: 2 +- create_time: '2023-11-16' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 0f044c9f62773a88 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.eu/published/workflow?id=0f044c9f62773a88 + name: Assembly-decontamination-VGP9 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 075c4126e66def01 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=075c4126e66def01 + name: Scaffolding-BioNano-VGP7 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 0444c98a3ca2a3ca + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=0444c98a3ca2a3ca + name: Purge-duplicate-contigs-VGP6 (release v0.3.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 3010ecad1a342331 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=3010ecad1a342331 + name: Scaffolding-HiC-VGP8 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 71c4ec4805f83cd5 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=71c4ec4805f83cd5 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: db03a18167f26399 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=db03a18167f26399 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 45c5e0a1e10edc54 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=45c5e0a1e10edc54 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 1e02a7292e9974b1 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=1e02a7292e9974b1 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: acd29212884f967b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=acd29212884f967b + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: acfc7d1b03d5fbd0 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=acfc7d1b03d5fbd0 + name: kmer-profiling-hifi-VGP1 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - 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Remove beginning1 + - tp_cat + - Grouping1 + - cat1 + - tp_head_tool + - Grep1 + - regex1 + update_time: '2023-11-10' + versions: 5 +- create_time: '2023-10-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 89ff2a1143954d83 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=89ff2a1143954d83 + name: Ecoregionalization on Antarctic sea + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ecoregion_eco_map + - ecoregion_cluster_estimate + - ecoregion_clara_cluster + - ecoregion_brt_analysis + - ecoregion_taxa_seeker + update_time: '2023-11-09' + versions: 3 +- create_time: '2023-11-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: da88448ab15d167d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=da88448ab15d167d + name: Remote sensing Sentinel 2 data analysis to produce biodiversity metrics + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - srs_diversity_maps + - srs_global_indices + - srs_spectral_indices + - srs_preprocess_s2 + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a0404f6291874c01 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a0404f6291874c01 + name: Biodiversity data exploration tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ecology_stat_presence_abs + - ecology_link_between_var + - ecology_beta_diversity + - tool_anonymization + - ecology_homogeneity_normality + - ecology_presence_abs_abund + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence analysis + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: afad9a17a80bb26d + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d + name: Obitools eDNA metabarcoding + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - 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Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 270b6f82efab28b2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=270b6f82efab28b2 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 002a51bdef00e14d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: a6dd62ab4b9a0725 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=a6dd62ab4b9a0725 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 5bb7691b176d1010 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=5bb7691b176d1010 + name: Scaffolding-BioNano-VGP7 (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 11ce7a7bf3d075e0 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=11ce7a7bf3d075e0 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: d1e3d3bb0922d771 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=d1e3d3bb0922d771 + name: kmer-profiling-hifi-VGP1 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 3788bb24b97f7b83 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=3788bb24b97f7b83 + name: kmer-profiling-hifi-VGP1 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: bac84a7033c3423f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=bac84a7033c3423f + name: Purge-duplicate-contigs-VGP6 (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 915ffef5b14c871e + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=915ffef5b14c871e + name: Purge duplicate contigs (WF6 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: ca39822372847670 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=ca39822372847670 + name: Purge duplicate contigs (WF6 (release v0.2.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 9667bf36217083b7 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=9667bf36217083b7 + name: Purge-duplicate-contigs-VGP6 (release v0.3.0) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: bc8ccd13a07bd9ec + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=bc8ccd13a07bd9ec + name: Scaffolding-HiC-VGP8 (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: c8f94a2e838fc0f1 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=c8f94a2e838fc0f1 + name: Scaffolding-HiC-VGP8 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-07' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: cf196794bbd365d8 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8 + name: feature_extraction + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ip_2d_split_binaryimage_by_watershed + - ip_threshold + - ip_2d_filter_segmentation_by_features + - ip_filter_standard + - ip_2d_feature_extraction + update_time: '2023-11-07' + versions: 3 +- create_time: '2023-08-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 81033ff723b9f22d + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=81033ff723b9f22d + name: Main Metatranscriptomics Analysis 24.08.2023 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + tools: [] + update_time: '2023-11-07' + versions: 6 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: cdf782de6c67477a + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=cdf782de6c67477a + name: baredSC_2d_logN (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2023-11-02' + versions: 1 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 72c03f7b5bc9fb9d + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=72c03f7b5bc9fb9d + name: baredSC_1d_logN (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2023-11-02' + versions: 1 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 14b9753269cd368f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=14b9753269cd368f + name: ChIPseq_SR (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-11-02' + versions: 1 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d83280cd72ec0f33 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d83280cd72ec0f33 + name: ATACseq (release v0.7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-11-02' + versions: 1 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 111527fe542846af + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=111527fe542846af + name: ATACseq (release v0.8) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-11-02' + versions: 1 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7e0ba4c14803448e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7e0ba4c14803448e + name: ATACseq (release v0.9) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-11-02' + versions: 1 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 79fd2517af48c594 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=79fd2517af48c594 + name: ChIPseq_PE (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-11-02' + versions: 1 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5138874b208adb4b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5138874b208adb4b + name: CUTandRUN (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-02' + versions: 1 +- create_time: '2023-11-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 74e4a8f2edb25f1a + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=74e4a8f2edb25f1a + name: CUTandRUN (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-02' + versions: 1 +- create_time: '2021-07-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ca342c5018c210e7 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=ca342c5018c210e7 + name: 3_Microbial Peptides PepQuery Validation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Grouping1 + - pepquery + - Cut1 + - Filter1 + update_time: '2023-10-31' + versions: 6 +- create_time: '2023-10-26' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - SNP annotation + edam_topic: [] + id: ce1712139b4a4273 + latest_version: 15 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273 + name: Cancer variant annotation (hg38 VEP-based) with MAF export + number_of_steps: null + source: https://usegalaxy.eu + tags: + - EOSC4Cancer + tools: + - tp_text_file_with_recurring_lines + - snpSift_filter + - snpSift_extractFields + - __EXTRACT_DATASET__ + - ensembl_vep + - collapse_dataset + - split_file_to_collection + - __RELABEL_FROM_FILE__ + - tp_tail_tool + - tp_replace_in_column + - tp_find_and_replace + - datamash_ops + - bcftools_plugin_split_vep + - compose_text_param + - export_remote + - __MERGE_COLLECTION__ + - vcfanno + - Add_a_column1 + - __SORTLIST__ + - __FILTER_FROM_FILE__ + - vcf2maf + - param_value_from_file + - __BUILD_LIST__ + - datamash_transpose + - Filter1 + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - tp_easyjoin_tool + update_time: '2023-10-27' + versions: 15 +- create_time: '2023-10-26' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: af30010868c97316 + latest_version: 13 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=af30010868c97316 + name: Variant calling from matched tumor/normal sample pair (hg38 version) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - EOSC4Cancer + tools: + - fastqc + - tp_text_file_with_recurring_lines + - trimmomatic + - __EXTRACT_DATASET__ + - split_file_to_collection + - collapse_dataset + - __RELABEL_FROM_FILE__ + - varscan_somatic + - Grep1 + - Convert characters1 + - compose_text_param + - samtools_calmd + - multiqc + - tp_replace_in_line + - samtools_rmdup + - qualimap_bamqc + - __APPLY_RULES__ + - __BUILD_LIST__ + - pick_value + - bwa_mem + - bamleftalign + - samtools_view + update_time: '2023-10-27' + versions: 13 +- create_time: '2023-10-26' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 6aaf2b342d57f78d + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6aaf2b342d57f78d + name: sra_manifest_to_concatenated_fastqs_ (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2023-10-26' + versions: 1 +- create_time: '2023-10-26' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 92760fc19ef120ce + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=92760fc19ef120ce + name: Assembly-Hifi-only-VGP3 (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2023-10-26' + versions: 1 +- create_time: '2023-10-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5374daf356516a40 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=5374daf356516a40 + name: WF3-Verification Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - pepquery2 + - Remove beginning1 + - Cut1 + - collapse_dataset + - tp_cat + - query_tabular + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - uniprotxml_downloader + - dbbuilder + - Filter1 + update_time: '2023-10-25' + versions: 6 +- create_time: '2023-10-21' + creators: + - Julia Jakiela + doi: '' + edam_operation: [] + edam_topic: [] + id: 1d4e81b51eae43c4 + latest_version: 3 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4 + name: EBI Single Cell Expression Atlas files to AnnData + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_read_10x + - regexColumn1 + - tp_grep_tool + - anndata_ops + - retrieve_scxa + update_time: '2023-10-21' + versions: 3 +- create_time: '2023-10-18' + creators: + - Marius van den Beek + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Primer removal + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: bc79a9f797334b01 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=bc79a9f797334b01 + name: miRNA differential expression + number_of_steps: null + source: https://usegalaxy.eu + tags: + - miRNA + tools: + - fastqc + - trim_galore + - __TAG_FROM_FILE__ + - volcanoplot + - bowtie2 + - featurecounts + - deseq2 + update_time: '2023-10-20' + versions: 8 +- create_time: '2023-10-03' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: d148459a4d4b91f1 + latest_version: 12 + license: null + link: https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1 + name: WF5_Data-interpretation-worklow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - msstatstmt + - Grep1 + - unipept + update_time: '2023-10-19' + versions: 12 +- create_time: '2023-10-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: d789165f4e0c50eb + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=d789165f4e0c50eb + name: WF4_Quantitation_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Grouping1 + - Grep1 + - maxquant + - Cut1 + update_time: '2023-10-19' + versions: 1 +- create_time: '2023-10-19' + creators: + - Matthias Bernt + doi: '' + edam_operation: [] + edam_topic: [] + id: e9e41c23261d4ac5 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=e9e41c23261d4ac5 + name: MetaProSIP OpenMS 2.8 (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - FalseDiscoveryRate + - FeatureFinderMultiplex + - IDMapper + - MSGFPlusAdapter + - DecoyDatabase + - MetaProSIP + - __SORTLIST__ + - PeptideIndexer + update_time: '2023-10-19' + versions: 1 +- create_time: '2023-10-13' + creators: + - Wendi Bacon + - Julia Jakiela + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 8ce45d9ca1b62624 + latest_version: 4 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=8ce45d9ca1b62624 + name: Filter, Plot and Explore Single-cell RNA-seq Data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:training + - name:single-cell + tools: + - anndata_manipulate + - scanpy_find_cluster + - scanpy_scale_data + - anndata_inspect + - scanpy_compute_graph + - scanpy_find_markers + - scanpy_plot_embed + - Cut1 + - scanpy_normalise_data + - join1 + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_plot + - anndata_ops + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2023-10-13' + versions: 4 +- create_time: '2023-10-10' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - SNP annotation + edam_topic: [] + id: 2424282f793f0f1b + latest_version: 10 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b + name: Cancer variant annotation (hg38 VEP-based) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - EOSC4Cancer + tools: + - tp_text_file_with_recurring_lines + - snpSift_filter + - snpSift_extractFields + - __EXTRACT_DATASET__ + - ensembl_vep + - collapse_dataset + - split_file_to_collection + - __RELABEL_FROM_FILE__ + - tp_replace_in_column + - tp_find_and_replace + - datamash_ops + - bcftools_plugin_split_vep + - __MERGE_COLLECTION__ + - vcfanno + - Add_a_column1 + - __SORTLIST__ + - __FILTER_FROM_FILE__ + - vcf2maf + - __BUILD_LIST__ + - datamash_transpose + - Filter1 + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - tp_easyjoin_tool + update_time: '2023-10-10' + versions: 10 +- create_time: '2023-10-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: f53b5a60763d85b6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=f53b5a60763d85b6 + name: Average Bigwig between replicates (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - deeptools_bigwig_average + - __APPLY_RULES__ + update_time: '2023-10-05' + versions: 1 +- create_time: '2023-10-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d12617d0df5f81d0 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d12617d0df5f81d0 + name: ATACseq (release v0.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-10-05' + versions: 1 +- create_time: '2023-10-05' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 6478043c474ac82e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6478043c474ac82e + name: Parallel Accession Down (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-10-05' + versions: 1 +- create_time: '2023-09-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Heat map generation + - Filtering + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: 607ca3a9d45bd080 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080 + name: WF2_Discovery-Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ident_params + - maxquant + - fasta_cli + - filter_tabular + - Cut1 + - Remove beginning1 + - tp_cat + - query_tabular + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - Grep1 + - search_gui + - peptide_shaker + - dbbuilder + - msconvert + - Filter1 + update_time: '2023-10-03' + versions: 5 +- create_time: '2023-09-07' + creators: [] + doi: '' + edam_operation: + - Target-Decoy + - de Novo sequencing + - Tag-based peptide identification + - Expression analysis + - Protein identification + edam_topic: [] + id: 2f7e13eb26c8cd18 + latest_version: 10 + license: null + link: https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18 + name: WF1_Database Generation Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - metanovo + - fasta_merge_files_and_filter_unique_sequences + update_time: '2023-10-03' + versions: 10 +- create_time: '2023-09-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 3b1f0473ec89aa00 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3b1f0473ec89aa00 + name: Average Bigwig between replicates (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - deeptools_bigwig_average + - __APPLY_RULES__ + update_time: '2023-09-28' + versions: 1 +- create_time: '2023-09-28' + creators: + - Romane Libouban + doi: '' + edam_operation: + - Genome annotation + - Repeat sequence detection + edam_topic: [] + id: 09c534f738426a6d + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=09c534f738426a6d + name: Repeat masking with RepeatModeler and RepeatMask (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - repeatmasker_wrapper + - repeatmodeler + update_time: '2023-09-28' + versions: 1 +- create_time: '2023-09-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8132c3b710fd6d48 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=8132c3b710fd6d48 + name: ATACseq (release v0.5.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-09-28' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: cbe9e09ed3e91e2e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=cbe9e09ed3e91e2e + name: Hi-C_fastqToPairs_hic (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - hicup2juicer + - compose_text_param + - hicup_hicup + - Filter1 + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6ebd09100fc98878 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6ebd09100fc98878 + name: RNAseq_PE (release v0.4.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 406e6ef0dfb38628 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=406e6ef0dfb38628 + name: RNAseq_PE (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d3edc3f0659a5e5b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d3edc3f0659a5e5b + name: RNAseq_SR (release v0.4.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: bace9aebab9d4ce3 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=bace9aebab9d4ce3 + name: RNAseq_SR (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 51cce3b98da3e822 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=51cce3b98da3e822 + name: Arquea workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - Cut1 + - Add_a_column1 + - gops_join_1 + - join1 + - CONVERTER_uncompressed_to_gz + - Grouping1 + - Paste1 + - Extract genomic DNA 1 + update_time: '2023-09-20' + versions: 4 +- create_time: '2023-09-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7878623b7e959284 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=7878623b7e959284 + name: RasgosFlow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - Add_a_column1 + - gops_join_1 + - join1 + - Grouping1 + - tp_cut_tool + - tp_head_tool + - build_ucsc_custom_track_1 + - comp1 + update_time: '2023-09-19' + versions: 3 +- create_time: '2023-09-12' + creators: + - Marisa Loach + doi: '' + edam_operation: [] + edam_topic: [] + id: decd6ad0b41289ef + latest_version: 7 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=decd6ad0b41289ef + name: Inferring Trajectories with Scanpy Tutorial Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + tools: + - anndata_manipulate + - scanpy_run_dpt + - scanpy_plot_embed + - scanpy_compute_graph + - scanpy_run_paga + - scanpy_run_fdg + - scanpy_plot_trajectory + - scanpy_run_diffmap + update_time: '2023-09-19' + versions: 7 +- create_time: '2023-09-14' + creators: + - Anna Syme + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Mapping assembly + edam_topic: [] + id: a4f50449afde4a05 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a4f50449afde4a05 + name: Assembly polishing with long reads (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + - racon + update_time: '2023-09-14' + versions: 1 +- create_time: '2023-09-13' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Sequence alignment + - Genome alignment + - Generation + - Filtering + - Read mapping + - Genome indexing + - Sequencing quality control + edam_topic: [] + id: 3fb550d7c2bc390a + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a + name: Workflow constructed from history 'LSDV analysis development' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - read_it_and_keep + - qualimap_bamqc + - fasta_regex_finder + - ivar_consensus + - samtools_view + - bwa_mem + update_time: '2023-09-13' + versions: 2 +- create_time: '2023-07-13' + creators: [] + doi: '' + edam_operation: + - Target-Decoy + - de Novo sequencing + - Tag-based peptide identification + - Expression analysis + - Protein identification + edam_topic: [] + id: c6aecbdbeb27585f + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f + name: Clinical-MP-Database generation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - metanovo + - dbbuilder + - uniprotxml_downloader + - fasta_merge_files_and_filter_unique_sequences + update_time: '2023-09-07' + versions: 7 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 5385abe9c2589b69 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5385abe9c2589b69 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 16080c3c1488a8b5 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=16080c3c1488a8b5 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 0fb12e3a127fc4be + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0fb12e3a127fc4be + name: Get Confident Peaks From ChIP_SR duplicates (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 1214523f54a999fc + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1214523f54a999fc + name: Hi-C_juicermediumtabixToCool_c (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_balance + - cooler_makebins + - cooler_cload_tabix + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 7d49f41cd294e15b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7d49f41cd294e15b + name: Hi-C_fastqToPairs_hic (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - hicup2juicer + - compose_text_param + - hicup_hicup + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: fc4e3479d86f9a26 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=fc4e3479d86f9a26 + name: Hi-C_juicermediumtabixToCool_c (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_balance + - cooler_makebins + - cooler_cload_tabix + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 9f8a93cfffb31cd6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9f8a93cfffb31cd6 + name: cHi-C_fastqToCool_hicup_c (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + - compose_text_param + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 506a451679fe25b4 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=506a451679fe25b4 + name: Hi-C_fastqToCool_hicup_c (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 83fea2e4508bc3ed + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=83fea2e4508bc3ed + name: Hi-C_fastqToPairs_hic (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - hicup2juicer + - compose_text_param + - hicup_hicup + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: f394d1b12779ba41 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=f394d1b12779ba41 + name: cHi-C_fastqToCool_hicup_c (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + - compose_text_param + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 72201ffaf488f278 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=72201ffaf488f278 + name: Hi-C_fastqToCool_hicup_c (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 54b91dd86f463391 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=54b91dd86f463391 + name: ATACseq (release v0.5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 146cef3acb2eba75 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=146cef3acb2eba75 + name: CUTandRUN (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 08e50a41a8571c15 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=08e50a41a8571c15 + name: Parallel Accession Down (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 996b0499d98b1869 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=996b0499d98b1869 + name: sequence mapping + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: [] + update_time: '2023-09-06' + versions: 0 +- create_time: '2023-04-08' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + - Genome assembly + - Read mapping + - Coding region prediction + - Scaffolding + - Sequence contamination filtering + - Analysis + - Visualisation + - Gene prediction + - Genome annotation + - Transcriptome assembly + - Read alignment + - Sequence assembly + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 007ce6405d196df3 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=007ce6405d196df3 + name: WGS Illumina for Microbiome (comprehensive) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - pilon + - taxonomy_krona_chart + - staramr_search + - quast + - spades + - prokka + - kraken2 + - bowtie2 + - busco + update_time: '2023-09-03' + versions: 6 +- create_time: '2023-03-16' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 204854b8ec94da85 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=204854b8ec94da85 + name: Exploring Iris dataset with statistics and scatterplots + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2023-09-01' + versions: 3 +- create_time: '2023-08-31' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 57b96a59cca0e8df + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=57b96a59cca0e8df + name: Hi-C_fastqToPairs_hic (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - hicup2juicer + - compose_text_param + - hicup_hicup + - Filter1 + update_time: '2023-08-31' + versions: 1 +- create_time: '2023-08-31' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fa0ff9a0db8bbddb + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=fa0ff9a0db8bbddb + name: ChIPseq_SR (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-08-31' + versions: 1 +- create_time: '2023-08-31' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fd6429a788660c8d + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=fd6429a788660c8d + name: ChIPseq_PE (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-08-31' + versions: 1 +- create_time: '2023-08-23' + creators: [] + doi: '' + edam_operation: + - Read mapping + - Sequence clustering + - Read binning + edam_topic: [] + id: 58f779d238d569dc + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=58f779d238d569dc + name: CONCOCT + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - concoct_merge_cut_up_clustering + - samtools_sort + - concoct_coverage_table + - concoct_cut_up_fasta + - concoct + - concoct_extract_fasta_bins + - samtools_view + - bowtie2 + update_time: '2023-08-28' + versions: 2 +- create_time: '2023-08-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9f3a6237aa09f3cb + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=9f3a6237aa09f3cb + name: test_cond_wf_short + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_cat + update_time: '2023-08-22' + versions: 6 +- create_time: '2023-01-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cc483bb070e57474 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=cc483bb070e57474 + name: GPU_Jupyterlab_tool_workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - interactive_tool_ml_jupyter_notebook + - Cut1 + - Filter1 + update_time: '2023-08-17' + versions: 3 +- create_time: '2023-08-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 533700cbfc4988c3 + latest_version: 19 + license: null + link: https://usegalaxy.eu/published/workflow?id=533700cbfc4988c3 + name: main + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: [] + update_time: '2023-08-08' + versions: 19 +- create_time: '2023-07-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c4cefff5b812aae9 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=c4cefff5b812aae9 + name: peaks to genes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Grouping1 + - gops_intersect_1 + update_time: '2023-07-30' + versions: 1 +- create_time: '2023-07-29' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Visualisation + - Taxonomic classification + - Genome assembly + - Sequence composition calculation + - Aggregation + - Sequencing quality control + edam_topic: [] + id: b37800d990cceb83 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=b37800d990cceb83 + name: Copy of Copy of Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastp + - taxonomy_krona_chart + - krakentools_kreport2krona + - kraken2 + - megahit + update_time: '2023-07-29' + versions: 0 +- create_time: '2023-07-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0edf0e9a778cb732 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=0edf0e9a778cb732 + name: From peaks to genes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Grouping1 + - gops_intersect_1 + - tp_sort_header_tool + update_time: '2023-07-27' + versions: 3 +- create_time: '2023-07-25' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 63eed9c2e025a723 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=63eed9c2e025a723 + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - snpSift_extractFields + - collapse_dataset + - tp_sort_header_tool + - lofreq_call + - multiqc + - bwa_mem + update_time: '2023-07-25' + versions: 2 +- create_time: '2023-07-24' + creators: [] + doi: '' + edam_operation: + - Classification + - Visualisation + - Taxonomic classification + edam_topic: [] + id: 2e5e6291cd112225 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=2e5e6291cd112225 + name: ' ''EXAMEN BIOINFORMATICA''' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - 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variant-analysis + tools: + - pyega3 + - CONVERTER_gz_to_uncompressed + - gemini_inheritance + - gemini_load + - regexColumn1 + - CONVERTER_uncompressed_to_gz + - tp_grep_tool + - gene_iobio_display_generation_iframe + - bcftools_norm + - bcftools_merge + - snpEff + - Filter1 + update_time: '2023-07-11' + versions: 76 +- create_time: '2023-07-10' + creators: + - Genthon, Tanguy + doi: '' + edam_operation: [] + edam_topic: [] + id: c620fc0244be645d + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=c620fc0244be645d + name: Metashrimps + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Metadata + - FAIR + - Data + - Paper + tools: + - interactive_tool_metashrimps + update_time: '2023-07-10' + versions: 2 +- create_time: '2023-03-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cb3d961914ede12e + latest_version: 62 + license: null + link: https://usegalaxy.eu/published/workflow?id=cb3d961914ede12e + name: SVM classifier with SelectFdr feature selection - no test labels as input + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - table_compute + - comp1 + - sklearn_feature_selection + - sklearn_data_preprocess + - sklearn_build_pipeline + - csv_to_tabular + - model_prediction + - tp_cut_tool + - cat1 + - tp_head_tool + - datamash_transpose + - sklearn_searchcv + update_time: '2023-07-10' + versions: 62 +- create_time: '2023-07-07' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: fa670d951fc4f778 + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=fa670d951fc4f778 + name: Example - Reference Genome Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snpSift_filter + - trimmomatic + - bowtie2 + - freebayes + update_time: '2023-07-08' + versions: 13 +- create_time: '2023-07-07' + creators: + - "B\xE9r\xE9nice Batut" + - Pratik Jagtap + - Subina Mehta + - Ray Sajulga + - Emma Leith + - Praveen Kumar + - Saskia Hiltemann + - Paul Zierep + - Engy Nasr + doi: '' + edam_operation: + - Phylogenetic analysis + - Taxonomic classification + - Species frequency estimation + edam_topic: [] + id: a7a6d8ecc2795f58 + latest_version: 3 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 + name: pAllori ASiam Functional Information MT + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:metatranscriptomics + - name:AdaptedASiam + - name:functionalProfiling + tools: + - humann_split_stratified_table + - Cut1 + - combine_metaphlan2_humann2 + - Grep1 + - tp_find_and_replace + - humann_renorm_table + - humann + - humann_unpack_pathways + - humann_rename_table + - humann_regroup_table + update_time: '2023-07-07' + versions: 3 +- create_time: '2023-06-30' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Taxonomic classification + - Phylogenetic inference + - Phylogenetic tree visualisation + - Visualisation + - Conversion + - Phylogenetic tree analysis + - Nucleic acid sequence analysis + - Phylogenetic tree editing + edam_topic: [] + id: 05f5f040337786bf + latest_version: 3 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=05f5f040337786bf + name: ' pAllori ASiam Community Profile MT' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:metatranscriptomics + - name:AdaptedASiam + - name:communityProfiling + tools: + - taxonomy_krona_chart + - Cut1 + - export2graphlan + - graphlan + - graphlan_annotate + - metaphlan + update_time: '2023-07-06' + versions: 3 +- create_time: '2023-06-30' + creators: + - "B\xE9r\xE9nice Batut" + - Pratik Jagtap + - Subina Mehta + - Ray Sajulga + - Emma Leith + - Praveen Kumar + - Saskia Hiltemann + - Paul Zierep + - Engy Nasr + doi: '' + edam_operation: + - Statistical calculation + - Sequence alignment analysis + - Sequence composition calculation + - Sequence comparison + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence similarity search + - Sequencing quality control + edam_topic: [] + id: 72e3e5fdc766e24a + latest_version: 2 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a + name: ' pAllori ASiam Preprocessing MT' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microGalaxy + - name:AdaptedASiam + - name:metatranscriptomics + - name:preprocessing + tools: + - fastqc + - fastq_paired_end_interlacer + - cutadapt + - __FLATTEN__ + - multiqc + - bg_sortmerna + update_time: '2023-07-06' + versions: 2 +- create_time: '2023-07-04' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Taxonomic classification + - Sequencing quality control + edam_topic: [] + id: 4a39d38fde81e35d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=4a39d38fde81e35d + name: Collection Implicit conversion Example + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - seq_filter_by_id + - filter_tabular + - kraken2 + - porechop + update_time: '2023-07-04' + versions: 1 +- create_time: '2023-01-21' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + edam_topic: [] + id: 513389e1a8c6bba9 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9 + name: Workflow constructed from history 'Test Pipeline 21Jan23' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - obi_uniq + - seq_filter_by_id + - obi_tab + - obi_clean + - obi_annotate + - join1 + - obi_stat + - ncbi_blastn_wrapper + - obi_grep + - obi_illumina_pairend + update_time: '2023-06-30' + versions: 0 +- create_time: '2023-06-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: eeb6cff210cac091 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091 + name: Clinical_Metaproteomics_1_Large Database Generation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - dbbuilder + - uniprotxml_downloader + - fasta_merge_files_and_filter_unique_sequences + update_time: '2023-06-20' + versions: 2 +- create_time: '2023-06-16' + creators: + - Wolfgang Maier + - Sebastian Holler + doi: '' + edam_operation: + - SNP annotation + edam_topic: [] + id: 1da86d74f8535f4e + latest_version: 9 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e + name: Somatic variant annotation and reporting from WES tumor/normal sample pairs + (hg38) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cancer + tools: + - tp_text_file_with_recurring_lines + - snpSift_filter + - snpSift_extractFields + - __EXTRACT_DATASET__ + - ensembl_vep + - collapse_dataset + - split_file_to_collection + - __RELABEL_FROM_FILE__ + - tp_replace_in_column + - tp_find_and_replace + - datamash_ops + - bcftools_plugin_split_vep + - __MERGE_COLLECTION__ + - vcfanno + - Add_a_column1 + - __SORTLIST__ + - __FILTER_FROM_FILE__ + - vcf2maf + - __BUILD_LIST__ + - datamash_transpose + - Filter1 + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - tp_easyjoin_tool + update_time: '2023-06-19' + versions: 9 +- create_time: '2023-06-16' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Genome alignment + - Sequence composition calculation + - Genome indexing + - Read mapping + - Variant calling + - Validation + - Copy number estimation + - Generation + - Sequencing quality control + - Sequence alignment + - Sequence visualisation + edam_topic: [] + id: 2c3d05023c02113e + latest_version: 11 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e + name: Somatic variant discovery from WES tumor/normal sample pairs (hg38) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cancer + tools: + - fastqc + - tp_text_file_with_recurring_lines + - trimmomatic + - __EXTRACT_DATASET__ + - split_file_to_collection + - collapse_dataset + - __RELABEL_FROM_FILE__ + - control_freec + - varscan_somatic + - Grep1 + - Convert characters1 + - compose_text_param + - samtools_calmd + - multiqc + - Add_a_column1 + - tp_replace_in_line + - samtools_rmdup + - qualimap_bamqc + - __APPLY_RULES__ + - param_value_from_file + - __BUILD_LIST__ + - circos + - bwa_mem + - Cut1 + - add_line_to_file + - bamleftalign + - samtools_view + update_time: '2023-06-19' + versions: 11 +- create_time: '2023-06-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c696b37d1bf68e9b + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=c696b37d1bf68e9b + name: Workflow constructed from history 'generate training material' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - addValue + - fasta2tab + - fasta_compute_length + update_time: '2023-06-15' + versions: 2 +- create_time: '2023-05-16' + creators: + - "Crist\xF3bal Gallardo Alba" + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - De-novo assembly + - Sequence composition calculation + - Sequence comparison + - Sequence annotation + - Validation + - Sequence contamination filtering + - RNA-Seq analysis + - Transcriptome assembly + - Sequence analysis + - Sequence assembly validation + - Sequence alignment + - Protein sequence analysis + - Sequencing quality control + edam_topic: [] + id: 9b025479fade745d + latest_version: 103 + license: CC-BY-SA-4.0 + link: https://usegalaxy.eu/published/workflow?id=9b025479fade745d + name: Genome-wide alternative splicing analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:alternative_splicing + - name:GTN + - name:transcriptomics + tools: + - fastqc + - rseqc_inner_distance + - tp_sorted_uniq + - stringtie_merge + - rseqc_junction_annotation + - rseqc_junction_saturation + - Remove beginning1 + - tp_sort_header_tool + - stringtie + - pfamscan + - tp_grep_tool + - rseqc_infer_experiment + - __FLATTEN__ + - rna_quast + - rna_star + - multiqc + - gene2exon1 + - sort1 + - fastp + - gtftobed12 + - tp_cat + - rseqc_geneBody_coverage + - tp_awk_tool + - __FILTER_FROM_FILE__ + - param_value_from_file + - gffread + - Cut1 + - rseqc_read_distribution + - cpat + - isoformswitchanalyzer + update_time: '2023-06-11' + versions: 103 +- create_time: '2022-08-24' + creators: [] + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Coding region prediction + - Scaffolding + - Variant calling + - Genome annotation + - Visualisation + - Transcriptome assembly + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Gene prediction + - Sequence assembly + - Sequence assembly validation + - Scatter plot plotting + edam_topic: [] + id: cf8591391a17a914 + latest_version: 10 + license: null + link: https://usegalaxy.eu/published/workflow?id=cf8591391a17a914 + name: ONT genome assembly (prokaryote) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Nanopore + - WGS + tools: + - nanoplot + - quast + - medaka_consensus_pipeline + - flye + - prokka + - busco + update_time: '2023-06-08' + versions: 10 +- create_time: '2023-06-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Variant calling + - Sequence trimming + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: cc37667c2d1f9056 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056 + name: Workflow constructed from history 'Final Project-1' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gtftobed12 + - samtools_view + - samtools_idxstats + - rseqc_read_distribution + - fastq_dump + - rseqc_geneBody_coverage + - cutadapt + - __FLATTEN__ + - rseqc_infer_experiment + - rna_star + - multiqc + - picard_MarkDuplicates + - featurecounts + - freebayes + - hisat2 + update_time: '2023-06-06' + versions: 0 +- create_time: '2023-01-16' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Variant calling + - Pairwise sequence alignment + edam_topic: [] + id: 3f0b104a74acf869 + latest_version: 8 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869 + name: Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identification + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + - nanopore + tools: + - clair3 + - snpSift_filter + - snpSift_extractFields + - bcftools_norm + - minimap2 + - bcftools_consensus + update_time: '2023-05-30' + versions: 8 +- create_time: '2023-01-10' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + - Multilocus sequence typing + edam_topic: [] + id: 2b888e200dfd91bc + latest_version: 20 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc + name: Pathogen-Detection-Nanopore-Gene-based-pathogenic-Identification + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + - nanopore + tools: + - abricate + - medaka_consensus_pipeline + - Cut1 + - flye + - add_line_to_file + - fasta2tab + - mlst + - tp_replace_in_column + - cat1 + - tab2fasta + - compose_text_param + - tp_find_and_replace + - bandage_image + update_time: '2023-05-30' + versions: 20 +- create_time: '2023-02-02' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Taxonomic classification + edam_topic: [] + id: a0ea6fc756dd17ea + latest_version: 4 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea + name: Pathogen Detection-Nanopore-Taxonomy-Profiling-and-Visualization + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + - nanopore + tools: + - kraken2 + - interactive_tool_phinch + - kraken_biom + update_time: '2023-05-30' + versions: 4 +- create_time: '2023-02-17' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: ed2df13cfbc86b99 + latest_version: 6 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ed2df13cfbc86b99 + name: Pathogen-Detection-Nanopore-Taxonomy-Profiling-and-Visualization-with-krona + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + - nanopore + tools: + - kraken2 + - krakentools_kreport2krona + - krona-text + update_time: '2023-05-30' + versions: 6 +- create_time: '2023-02-02' + creators: + - "B\xE9r\xE9nice Batut" + - Engy Nasr + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Sequence composition calculation + - Validation + - Sequence contamination filtering + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: 889f2782ad82bd69 + latest_version: 6 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69 + name: Pathogen-Detection-Nanopore-Pre-Processing + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + - nanopore + tools: + - fastqc + - nanoplot + - fastp + - seq_filter_by_id + - filter_tabular + - kraken2 + - porechop + - multiqc + update_time: '2023-05-30' + versions: 6 +- create_time: '2023-05-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f5d387583670f694 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=f5d387583670f694 + name: Stacks RAD-seq de novo workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - stacks2_ustacks + - stacks2_cstacks + - stacks2_populations + - stacks2_gstacks + - stacks2_sstacks + - stacks2_tsv2bam + update_time: '2023-05-25' + versions: 2 +- create_time: '2023-05-22' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 25850714d13f0b0f + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=25850714d13f0b0f + name: Resistome workflow Pig Nov2021 (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Metagenomics + - Resistome + tools: + - fastp + - resistome_analyzer + - samtools_sort + - XY_Plot_1 + - bam_to_sam + - rarefaction_analyzer + - snpfinder + - bowtie2 + update_time: '2023-05-23' + versions: 0 +- create_time: '2023-05-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 86ae00e3d9ae2978 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=86ae00e3d9ae2978 + name: Workflow constructed from history 'Data Ommlycs Manipulation' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Count1 + - tp_sort_header_tool + - csv_to_tabular + - tabular_to_csv + - Filter1 + update_time: '2023-05-20' + versions: 0 +- create_time: '2023-05-20' + creators: + - "Crist\xF3bal Gallardo Alba" + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Sequence comparison + - Validation + - Sequence contamination filtering + - RNA-Seq analysis + - Transcriptome assembly + - Sequence analysis + - Sequence alignment + - Protein sequence analysis + - Sequencing quality control + edam_topic: [] + id: 1f9a9a7998ef5ab3 + latest_version: 0 + license: CC-BY-SA-4.0 + link: https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3 + name: Genome-wide alternative splicing analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:alternative_splicing + - name:GTN + - name:transcriptomics + tools: + - fastqc + - rseqc_junction_annotation + - rseqc_junction_saturation + - collection_element_identifiers + - Remove beginning1 + - stringtie + - pfamscan + - tp_grep_tool + - rseqc_infer_experiment + - __FLATTEN__ + - rna_star + - multiqc + - fastp + - gtftobed12 + - tp_cat + - rseqc_geneBody_coverage + - tp_awk_tool + - __FILTER_FROM_FILE__ + - rseqc_read_distribution + - cpat + - isoformswitchanalyzer + update_time: '2023-05-20' + versions: 0 +- create_time: '2023-04-25' + creators: [] + doi: '' + edam_operation: + - Formatting + edam_topic: [] + id: 4f40ae432d8a4259 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259 + name: Genomics + number_of_steps: null + source: https://usegalaxy.eu + tags: + - violethaze74 + - LMD-Genome + - violethaze74@jazzededtech.com + - violethaze74@aol.com + - violethaze74@gmail.com + - lmd1174 + - Face1174 + tools: + - CONVERTER_gz_to_uncompressed + - CONVERTER_interval_to_bed_0 + - ivar_variants + - blockbuster + - picard_FastqToSam + - Extract genomic DNA 1 + update_time: '2023-05-20' + versions: 2 +- create_time: '2023-05-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8f9bbda01c59673d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8f9bbda01c59673d + name: 'simo work flow ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - datamash_ops + - tabular_to_csv + - tp_sort_header_tool + update_time: '2023-05-19' + versions: 1 +- create_time: '2023-05-19' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: 7b2b1e08b8576e2e + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=7b2b1e08b8576e2e + name: Chioua's Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - samtools_view + - samtools_sort + - bowtie2 + - samtools_mpileup + update_time: '2023-05-19' + versions: 2 +- create_time: '2023-05-19' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: ca4e564da54d057b + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=ca4e564da54d057b + name: oumayma workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - samtools_view + - samtools_sort + - bowtie2 + - samtools_mpileup + update_time: '2023-05-19' + versions: 1 +- create_time: '2023-05-19' + creators: [] + doi: '' + edam_operation: + - 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Read summarisation + - Sequencing quality control + edam_topic: [] + id: e62b659a5da9734e + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e62b659a5da9734e + name: "An\xE1lisis de microRNAs" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastp + - fastq_dump + - featurecounts + - hisat2 + update_time: '2023-05-15' + versions: 1 +- create_time: '2023-05-15' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 1be0c4adf13cf368 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=1be0c4adf13cf368 + name: "An\xE1lisis de microRNAs" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastp + - fastq_dump + - featurecounts + - hisat2 + update_time: '2023-05-15' + versions: 1 +- create_time: '2023-04-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b26fee38f6f796d8 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=b26fee38f6f796d8 + name: ARRIBA + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rna_star + - fastqc + - trimmomatic + - fasterq_dump + update_time: '2023-05-08' + versions: 3 +- create_time: '2022-09-14' + creators: + - Julia Jakiela + doi: '' + edam_operation: [] + edam_topic: [] + id: f689faf267fbe504 + latest_version: 30 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=f689faf267fbe504 + name: Trajectory analysis using Monocle3 - full tutorial workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:trajectory_analysis + - name:transcriptomics + - name:scRNA-seq + - name:single_cell + tools: + - monocle3_partition + - monocle3_reduceDim + - monocle3_orderCells + - Cut1 + - anndata_inspect + - join1 + - regexColumn1 + - tp_cut_tool + - monocle3_plotCells + - monocle3_topmarkers + - monocle3_preprocess + - monocle3_learnGraph + - datamash_transpose + - monocle3_create + - monocle3_diffExp + - Filter1 + update_time: '2023-05-05' + versions: 30 +- create_time: '2023-04-24' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: dadca1020f586338 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=dadca1020f586338 + name: 'Training: 16S rRNA RNIMU' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + tools: + - mothur_heatmap_sim + - mothur_make_biom + - mothur_rarefaction_single + - mothur_align_seqs + - mothur_classify_seqs + - mothur_venn + - taxonomy_krona_chart + - mothur_make_shared + - newick_display + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_dist_shared + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_tree_shared + - mothur_unique_seqs + - mothur_classify_otu + - mothur_taxonomy_to_krona + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - XY_Plot_1 + - mothur_count_groups + - mothur_cluster_split + - mothur_sub_sample + - mothur_pre_cluster + update_time: '2023-04-27' + versions: 8 +- create_time: '2023-04-21' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + edam_topic: [] + id: 0a0b5aff6bd9689d + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=0a0b5aff6bd9689d + name: HelperArribaPipeline + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rna_star + update_time: '2023-04-21' + versions: 7 +- create_time: '2023-04-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Validation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 83049910e2cd5128 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=83049910e2cd5128 + name: Identification of somatic and germline variants from tumor and normal sample + pairs tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: + - variant-analysis + tools: + - fastqc + - samtools_calmd + - trimmomatic + - bg_column_arrange_by_header + - gemini_load + - bamFilter + - samtools_rmdup + - varscan_somatic + - tp_easyjoin_tool + - snpEff + - gemini_annotate + - gemini_query + - bamleftalign + - multiqc + - bwa_mem + update_time: '2023-04-17' + versions: 0 +- create_time: '2023-03-29' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - Format validation + - Sequence motif recognition + - Coding region prediction + - Data retrieval + - Sequence assembly + - Sequence assembly validation + - Sequencing quality control + - Protein feature detection + - Taxonomic classification + - Gene functional annotation + - Sequence composition calculation + - Database search + - Validation + - Sequence analysis + - Conversion + - Probabilistic sequence generation + - Multiple sequence alignment + - Sequence generation + - Gene prediction + edam_topic: [] + id: 3eaa913306c16146 + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=3eaa913306c16146 + name: MetaG_Galaxy_workshop + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - fasplit + - tp_cat + - hmmer_hmmscan + - checkm_lineage_wf + - tp_grep_tool + - tp_awk_tool + - fraggenescan + - __FILTER_FROM_FILE__ + - interproscan + - cat_bins + - kofamscan + update_time: '2023-04-14' + versions: 13 +- create_time: '2023-04-03' + creators: [] + doi: '' + edam_operation: + - Analysis + - Sequence assembly + - Read mapping + - Read alignment + edam_topic: [] + id: 3588c40cab9b4e1d + latest_version: 16 + license: null + link: https://usegalaxy.eu/published/workflow?id=3588c40cab9b4e1d + name: Phage Pilon Polishing + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - pilon + - bowtie2 + update_time: '2023-04-14' + versions: 16 +- create_time: '2023-04-12' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - Format validation + - Sequence motif recognition + - Coding region prediction + - Data retrieval + - Sequence assembly + - Sequence assembly validation + - Sequencing quality control + - Protein feature detection + - Taxonomic classification + - Gene functional annotation + - Sequence composition calculation + - Database search + - Validation + - Sequence analysis + - Conversion + - Probabilistic sequence generation + - Multiple sequence alignment + - Sequence generation + - Gene prediction + edam_topic: [] + id: 6416cfdbd5273063 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063 + name: Multi-omics Workshop Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - fasplit + - tp_cat + - hmmer_hmmscan + - checkm_lineage_wf + - tp_grep_tool + - tp_awk_tool + - fraggenescan + - __FILTER_FROM_FILE__ + - interproscan + - cat_bins + - kofamscan + update_time: '2023-04-12' + versions: 1 +- create_time: '2023-04-11' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 0e0be913c3e27022 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022 + name: Metaproteomics_GTN_IMS2023 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2023-04-11' + versions: 1 +- create_time: '2023-03-27' + creators: [] + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Sequence alignment analysis + - Genome assembly + - De-novo assembly + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Sequence alignment + - Sequence assembly validation + - Genotyping + edam_topic: [] + id: bc32937d505135ab + latest_version: 17 + license: null + link: https://usegalaxy.eu/published/workflow?id=bc32937d505135ab + name: Post-assembly workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - collapse_dataset + - genomescope + - pretext_snapshot + - bg_diamond_makedb + - tp_find_and_replace + - bellerophon + - hisat2 + - gfastats + - interactive_tool_blobtoolkit + - CONVERTER_gz_to_uncompressed + - blobtoolkit + - smudgeplot + - bg_diamond + - meryl + - bwa_mem2 + - jellyfish + - merqury + - pretext_map + - bandage_image + - busco + update_time: '2023-04-03' + versions: 17 +- create_time: '2023-03-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e299721eec23b557 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e299721eec23b557 + name: Fastq-to-Fasta + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cshl_fastx_reverse_complement + - fastq_to_fasta_python + - fastq_stats + update_time: '2023-03-29' + versions: 1 +- create_time: '2023-02-13' + creators: [] + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 3069c17b52decab4 + latest_version: 16 + license: null + link: https://usegalaxy.eu/published/workflow?id=3069c17b52decab4 + name: Post-assembly workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - blobtoolkit + - collapse_dataset + - merqury + - genomescope + - gfastats + - tp_find_and_replace + - ncbi_blastn_wrapper + - interactive_tool_blobtoolkit + - meryl + - busco + - hisat2 + update_time: '2023-03-27' + versions: 16 +- create_time: '2023-03-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: ceb0a029c6d33ec6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ceb0a029c6d33ec6 + name: Hi-C_juicermediumtabixToCool_c (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_balance + - cooler_makebins + - cooler_cload_tabix + update_time: '2023-03-23' + versions: 1 +- create_time: '2023-03-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 9fc8b89954c04ee1 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9fc8b89954c04ee1 + name: cHi-C_fastqToCool_hicup_c (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + - compose_text_param + - Filter1 + update_time: '2023-03-23' + versions: 1 +- create_time: '2023-03-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 2a9c812f59b7b36c + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2a9c812f59b7b36c + name: Hi-C_fastqToCool_hicup_c (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + update_time: '2023-03-23' + versions: 1 +- create_time: '2020-01-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: 96d198ed953449fd + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=96d198ed953449fd + name: MetaP + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microgalaxy + tools: + - maxquant + update_time: '2023-03-16' + versions: 2 +- create_time: '2023-02-10' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Statistical calculation + - Formatting + - Sequence profile generation + - Format validation + - Sequence motif recognition + - Primer removal + - Coding region prediction + - Data retrieval + - Sequence assembly + - Sequence assembly validation + - Sequencing quality control + - Protein feature detection + - Taxonomic classification + - Gene functional annotation + - Local alignment + - Sequence composition calculation + - Database search + - Validation + - Sequence analysis + - Visualisation + - Sequence trimming + - Conversion + - Probabilistic sequence generation + - Gene prediction + - Sequence generation + - Multiple sequence alignment + - Read pre-processing + edam_topic: [] + id: 6158c3b5fc12044e + latest_version: 22 + license: null + link: https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e + name: MetaG_extended + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microgalaxy + tools: + - fastqc + - sort1 + - quast + - kofamscan + - fasplit + - tp_cat + - trim_galore + - hmmer_hmmscan + - checkm_lineage_wf + - tp_grep_tool + - tp_awk_tool + - fraggenescan + - coverm_contig + - interproscan + - cat_bins + - maxbin2 + - coverm_genome + update_time: '2023-03-16' + versions: 22 +- create_time: '2022-01-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7b576a562031ff7e + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=7b576a562031ff7e + name: Workflow 'Biodiversity data exploration tuto' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ecology_stat_presence_abs + - ecology_link_between_var + - ecology_beta_diversity + - tool_anonymization + - ecology_homogeneity_normality + - ecology_presence_abs_abund + update_time: '2023-03-13' + versions: 2 +- create_time: '2023-03-12' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Sequence trimming + - Sequence alignment analysis + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: ff4d5beb6ce1809d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=ff4d5beb6ce1809d + name: eDNA Mito + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - cutadapt + - fastq_join + - bg_diamond + update_time: '2023-03-12' + versions: 1 +- create_time: '2023-02-20' + creators: + - Geoff Mitchell + doi: '' + edam_operation: + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 9e01e24c5e749365 + latest_version: 13 + license: AGPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=9e01e24c5e749365 + name: RNAseq Analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-03-07' + versions: 13 +- create_time: '2023-01-14' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 03be9d62e8e4a129 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=03be9d62e8e4a129 + name: Assembly with HiC (WF4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - PAG2023 + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-03-03' + versions: 1 +- create_time: '2023-03-02' + creators: + - Viktoria Isabel Schwarz + - Wolfgang Maier + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Genome indexing + - Read mapping + - Global alignment + - Validation + - Sequence contamination filtering + - Sequence analysis + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b77e3b08092fa73e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b77e3b08092fa73e + name: Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - pox + - virology + tools: + - 'EMBOSS: maskseq51' + - split_file_to_collection + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - fasta_compute_length + - collection_element_identifiers + - datamash_ops + - Grep1 + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - samtools_merge + - tp_cat + - tp_sed_tool + - __SORTLIST__ + - qualimap_bamqc + - __APPLY_RULES__ + - param_value_from_file + - bwa_mem + - Cut1 + - __ZIP_COLLECTION__ + - ivar_consensus + - samtools_view + update_time: '2023-03-02' + versions: 1 +- create_time: '2020-01-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence alignment analysis + - Gene expression profiling + - Sequence composition calculation + - Sequence comparison + - Primer removal + - Sequence trimming + - Read pre-processing + - Sequence similarity search + - Sequencing quality control + edam_topic: [] + id: 385cc7df70d7916b + latest_version: 16 + license: null + link: https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b + name: MetaT + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:microgalaxy + tools: + - fastqc + - collection_column_join + - __UNZIP_COLLECTION__ + - trim_galore + - kallisto_quant + - bg_sortmerna + update_time: '2023-02-27' + versions: 16 +- create_time: '2023-02-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d1fe868a20a3a0a3 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=d1fe868a20a3a0a3 + name: Trio Analysis - preprocessing [CINECA Workshop 2023] + number_of_steps: null + source: https://usegalaxy.eu + tags: + - variant-analysis + tools: + - CONVERTER_gz_to_uncompressed + - regexColumn1 + - bcftools_norm + - bcftools_merge + - Filter1 + update_time: '2023-02-25' + versions: 4 +- create_time: '2023-02-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f5005e80d9ffa109 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=f5005e80d9ffa109 + name: CUTandRUN (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-02-23' + versions: 1 +- create_time: '2023-02-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 941bc727b61c09ab + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=941bc727b61c09ab + name: From peaks to genes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Grouping1 + - gops_intersect_1 + update_time: '2023-02-20' + versions: 1 +- create_time: '2023-02-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8f677efac7100097 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8f677efac7100097 + name: EBI SC Expression Atlas Release 19 Analysis Pipeline v0.2.5 (Scanpy 1.8.1 + - droplet) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_read_10x + - scanpy_compute_graph + - __FILTER_FAILED_DATASETS__ + - scanpy_normalise_data + - join1 + - scanpy_filter_cells + - scanpy_find_variable_genes + - scanpy_multiplet_scrublet + - Remove beginning1 + - scanpy_scale_data + - scanpy_find_markers + - __MERGE_COLLECTION__ + - scanpy_run_pca + - tp_replace_in_line + - scanpy_run_tsne + - scanpy_run_umap + - anndata_ops + - __BUILD_LIST__ + - scanpy_find_cluster + - Cut1 + - bg_column_arrange_by_header + - scanpy_filter_genes + - scanpy_integrate_harmony + - scanpy_parameter_iterator + - scanpy_plot_scrublet + update_time: '2023-02-17' + versions: 1 +- create_time: '2023-02-12' + creators: + - Aitor Atxaerandio-Landa + doi: '' + edam_operation: + - Phylogenetic analysis + - Aggregation + - Coding region prediction + - Variant calling + - Genome annotation + - Antimicrobial resistance prediction + - Sequence assembly validation + - Sequencing quality control + - Taxonomic classification + - Genome assembly + - Phylogenetic tree generation + - Phylogenetic tree visualisation + - Sequence contamination filtering + - Sequence analysis + - Visualisation + - Validation + - Gene prediction + edam_topic: [] + id: 94c3d329c31c712f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f + name: Genomic Analysis Workflow v 1.0.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - wgs + - illumina + - workflow + - pathogen + tools: + - fastp + - quast + - snippy + - staramr_search + - abricate + - taxonomy_krona_chart + - shovill + - krakentools_kreport2krona + - sistr_cmd + - prokka + - kraken2 + - iqtree + - roary + - snippy_core + - snp_dists + - multiqc + - abricate_summary + update_time: '2023-02-12' + versions: 1 +- create_time: '2023-02-12' + creators: + - Aitor Atxaerandio-Landa + doi: '' + edam_operation: + - Phylogenetic analysis + - Taxonomic classification + - Genome assembly + - Phylogenetic tree generation + - Coding region prediction + - Phylogenetic tree visualisation + - Sequence contamination filtering + - Variant calling + - Visualisation + - Genome annotation + - Antimicrobial resistance prediction + - Sequence analysis + - Validation + - Gene prediction + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 628062a8cf93261f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=628062a8cf93261f + name: Genomic Analysis Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - WGS + - Illumina + - pathogen + - workflow + tools: + - fastp + - Kraken2Tax + - snippy + - quast + - staramr_search + - abricate + - taxonomy_krona_chart + - shovill + - sistr_cmd + - prokka + - kraken2 + - iqtree + - roary + - snippy_core + - snp_dists + - multiqc + - abricate_summary + update_time: '2023-02-12' + versions: 1 +- create_time: '2023-02-10' + creators: [] + doi: '' + edam_operation: + - Sequence comparison + - Sequence analysis + - Protein sequence analysis + edam_topic: [] + id: 11eba1b28ec87963 + latest_version: 16 + license: null + link: https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963 + name: Isoform analysis final version + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - pfamscan + - cpat + - cat1 + - tp_awk_tool + - isoformswitchanalyzer + update_time: '2023-02-11' + versions: 16 +- create_time: '2022-05-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Read mapping + - Validation + - Sequence contamination filtering + - Visualisation + - Sequence alignment + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 1860e02bcb894a64 + latest_version: 27 + license: null + link: https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64 + name: Illumina Genome Assembly (Mycovirus) with Mycovirus Database Filtering + number_of_steps: null + source: https://usegalaxy.eu + tags: + - genome-assembly + tools: + - fastqc + - samtools_fastx + - fastp + - bwa_mem2 + - quast + - samtools_view + - fasta_filter_by_length + - collapse_dataset + - fasta_merge_files_and_filter_unique_sequences + - ncbi_blastx_wrapper + - ncbi_blastn_wrapper + - ncbi_makeblastdb + - multiqc + - spades_rnaviralspades + - bowtie2 + update_time: '2023-02-10' + versions: 27 +- create_time: '2022-07-06' + creators: [] + doi: '' + edam_operation: + - Read mapping + - Data handling + edam_topic: [] + id: a52c5dd688def9ba + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=a52c5dd688def9ba + name: 'Pair Strand IdenIdentifier ' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:strandidentififier + - name:RNA-seq + tools: + - rseqc_infer_experiment + - fastq_groomer + - bowtie2 + update_time: '2023-02-10' + versions: 3 +- create_time: '2023-01-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Read mapping + - Primer removal + - Coding region prediction + - Variant calling + - Differential gene expression analysis + - Genome annotation + - Antimicrobial resistance prediction + - Sequence clustering + - Generation + - Sequencing quality control + - Taxonomic classification + - Genome indexing + - Sequence composition calculation + - Validation + - Sequence contamination filtering + - Sequence trimming + - Gene prediction + - Read pre-processing + - Sequence alignment + edam_topic: [] + id: 6a5c39c1d38a10c2 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2 + name: 'NGS: pipeline yersinia' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - vcffilter2 + - trim_galore + - krona-text + - bismark_bowtie2 + - kraken2 + - bismark_deduplicate + - multiqc + - metaphlan2krona + - abricate + - ngsutils_bam_filter + - prokka + - antismash + - bcftools_consensus + - gatk_count_covariates + - freebayes + - bwa_mem + - bamleftalign + - bismark_pretty_report + update_time: '2023-02-08' + versions: 8 +- create_time: '2023-02-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0e6e181234b48121 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=0e6e181234b48121 + name: Day2_Combining datasets after pre-processing - Input' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - anndata_manipulate + - scanpy_read_10x + - anndata_inspect + - Cut1 + - sceasy_convert + - tp_replace_in_column + - Paste1 + - anndata_ops + - retrieve_scxa + update_time: '2023-02-08' + versions: 1 +- create_time: '2023-02-07' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + edam_topic: [] + id: df455b86fff16116 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=df455b86fff16116 + name: Day 2_from fasta to matrix + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - join1 + - dropletutils_read_10x + - sceasy_convert + - _dropletBarcodePlot + - dropletutils_empty_drops + update_time: '2023-02-08' + versions: 1 +- create_time: '2023-02-08' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 37e51e215684bdcc + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=37e51e215684bdcc + name: Day3_Filter, Plot and Explore Single-cell RNA-seq Data + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - anndata_manipulate + - scanpy_find_cluster + - scanpy_scale_data + - anndata_inspect + - scanpy_compute_graph + - scanpy_find_markers + - scanpy_plot_embed + - Cut1 + - scanpy_normalise_data + - join1 + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_plot + - anndata_ops + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2023-02-08' + versions: 0 +- create_time: '2023-01-15' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: bb13f30a5562d30d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=bb13f30a5562d30d + name: VGP Bionano + number_of_steps: null + source: https://usegalaxy.eu + tags: + - PAG2023 + tools: + - param_value_from_file + - bionano_scaffold + - gfastats + update_time: '2023-02-07' + versions: 1 +- create_time: '2023-02-06' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: f39528391f22aab0 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f39528391f22aab0 + name: 'Workflow constructed from history ''test for training'' ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastq_filter + - fastq_groomer + update_time: '2023-02-06' + versions: 1 +- create_time: '2022-12-22' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 3d047ed984762ce8 + latest_version: 9 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=3d047ed984762ce8 + name: Scaffolding BioNano (WF7) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - param_value_from_file + - bionano_scaffold + - gfastats + update_time: '2023-02-03' + versions: 9 +- create_time: '2022-12-22' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 012762cb4acb068b + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.eu/published/workflow?id=012762cb4acb068b + name: Decontamination (WF9) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-02-02' + versions: 1 +- create_time: '2022-12-15' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 069d99391a69baf4 + latest_version: 19 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=069d99391a69baf4 + name: Scaffolding HiC YAHS (WF8a) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - bwa_mem2 + - sort1 + - __EXTRACT_DATASET__ + - Cut1 + - bedtools_bamtobed + - yahs + - pretext_snapshot + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-02-02' + versions: 19 +- create_time: '2021-04-30' + creators: [] + doi: '' + edam_operation: + - Formatting + - Data handling + - RNA-Seq quantification + - Primer removal + - Validation + - Sequence trimming + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a461ea397418f3aa + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=a461ea397418f3aa + name: SMART-Seq II + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - collection_column_join + - fastq_dump + - cutadapt + - rna_star + - multiqc + - picard_MarkDuplicates + - featurecounts + update_time: '2023-02-01' + versions: 4 +- create_time: '2022-08-07' + creators: + - '' + - '' + - "B\xE9r\xE9nice Batut" + - '' + - Engy Nasr + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Sequence composition calculation + - Validation + - Sequence contamination filtering + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: 57d3109f32defa3b + latest_version: 71 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b + name: Nanopore Datasets - Pre-Processing + number_of_steps: null + source: https://usegalaxy.eu + tags: + - microbiome + - nanopore + tools: + - fastqc + - nanoplot + - fastp + - seq_filter_by_id + - filter_tabular + - kraken2 + - porechop + - multiqc + update_time: '2023-01-29' + versions: 71 +- create_time: '2021-12-14' + creators: + - Yash Munnalal Gupta + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 5436eb1c430a38dd + latest_version: 2 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=5436eb1c430a38dd + name: Mitochondrial genome assembly _V2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - novoplasty + update_time: '2023-01-27' + versions: 2 +- create_time: '2022-12-14' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: a3f082ff30357040 + latest_version: 24 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=a3f082ff30357040 + name: Purgedups (WF6) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-01-26' + versions: 24 +- create_time: '2023-01-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cd1c3afd055779a8 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=cd1c3afd055779a8 + name: Training workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: [] + update_time: '2023-01-25' + versions: 3 +- create_time: '2023-01-03' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: f6a625946dea60fa + latest_version: 6 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=f6a625946dea60fa + name: Assembly (WF3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - busco + update_time: '2023-01-20' + versions: 6 +- create_time: '2023-01-19' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 23821870734575e9 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=23821870734575e9 + name: Project workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - multiqc + - rna_star + update_time: '2023-01-19' + versions: 3 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ef1d11b79a2e1727 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ef1d11b79a2e1727 + name: RNAseq_PE (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d3494c6124f820b2 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d3494c6124f820b2 + name: RNAseq_PE (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 86e2e2faa2e0bd46 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=86e2e2faa2e0bd46 + name: RNAseq_SR (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b323867a9efcc6c6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b323867a9efcc6c6 + name: ChIPseq_SR (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 25aa944237d7fb82 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=25aa944237d7fb82 + name: ATACseq (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c3eba26c5d7febff + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c3eba26c5d7febff + name: ATACseq (release v0.4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b9ad204395f7d931 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b9ad204395f7d931 + name: ChIPseq_PE (release v0.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-01-19' + versions: 1 +- create_time: '2022-12-13' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: 19bb57f8cfa48bb9 + latest_version: 12 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=19bb57f8cfa48bb9 + name: Assembly Trio (WF5) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - param_value_from_file + - busco + update_time: '2023-01-18' + versions: 12 +- create_time: '2023-01-11' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 0fef06a87389eb59 + latest_version: 0 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=0fef06a87389eb59 + name: K-mer profiling and QC (WF1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP + - PAG2023 + tools: + - meryl + - genomescope + update_time: '2023-01-17' + versions: 0 +- create_time: '2023-01-11' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - 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PAG2023 + tools: + - bwa_mem2 + - sort1 + - __EXTRACT_DATASET__ + - bedtools_bamtobed + - yahs + - pretext_snapshot + - gfastats + - pretext_map + - bellerophon + - param_value_from_file + - busco + update_time: '2023-01-17' + versions: 2 +- create_time: '2022-12-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 533819bcb5aa78c5 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=533819bcb5aa78c5 + name: Workflow constructed from history 'BE480 NGS Assignment' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bwa + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2023-01-16' + versions: 0 +- create_time: '2023-01-03' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 085c3a4c89d137b5 + latest_version: 7 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=085c3a4c89d137b5 + name: Assembly with HiC (WF4) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-01-09' + versions: 7 +- create_time: '2022-12-12' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 7f5da1ebd6673841 + latest_version: 16 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=7f5da1ebd6673841 + name: K-mer profiling and QC for Trio (WF2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - meryl + - genomescope + update_time: '2023-01-09' + versions: 16 +- create_time: '2023-01-03' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: ff16623a63ff5124 + latest_version: 3 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=ff16623a63ff5124 + name: K-mer profiling and QC (WF1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VGP_curated + tools: + - meryl + - genomescope + update_time: '2023-01-09' + versions: 3 +- create_time: '2023-01-09' + creators: [] + doi: '' + edam_operation: + - Mapping + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + - Validation + - Peak calling + - Differential binding analysis + - Sequencing quality control + edam_topic: [] + id: 7d44ea091d437edf + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf + name: 'FOXG1-NEUROD1 KD ChIP-seq: QC; mapping, peaks, plots' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:NEuROD1 + - name:FOXG1 + - name:NEuROD1 + - name:ChIP-seq + tools: + - deeptools_plot_coverage + - gops_subtract_1 + - tp_replace_in_column + - deeptools_plot_fingerprint + - deeptools_bigwig_compare + - bowtie2 + - chipseeker + - gops_concat_1 + - Remove beginning1 + - deeptools_bam_compare + - ggplot2_heatmap2 + - cat1 + - gops_cluster_1 + - multiqc + - bedtools_mergebed + - bedtools_slopbed + - macs2_callpeak + - samtools_flagstat + - addValue + - samtool_filter2 + - Filter1 + - deeptools_plot_heatmap + - diffbind + - deeptools_compute_matrix + - bedtools_sortbed + - bedtools_intersectbed + - deeptools_multi_bam_summary + - deeptools_plot_correlation + update_time: '2023-01-09' + versions: 0 +- create_time: '2023-01-05' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Visualisation + - Taxonomic classification + - Sequencing quality control + edam_topic: [] + id: 8ee3b635c1c380cd + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=8ee3b635c1c380cd + name: WF-QC + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - kraken2 + - fastp + - taxonomy_krona_chart + update_time: '2023-01-05' + versions: 8 +- create_time: '2023-01-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 290bc4120c2c5078 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=290bc4120c2c5078 + name: NCBI-Blast+ analysis against MAdLand DB + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_blastp_wrapper + - ncbi_blastx_wrapper + update_time: '2023-01-03' + versions: 2 +- create_time: '2022-12-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 591ebf913450f49e + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=591ebf913450f49e + name: Workflow constructed from history 'CA2 amy duffy 19360556' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bwa + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2022-12-21' + versions: 5 +- create_time: '2022-12-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5e3c352233aa7a52 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=5e3c352233aa7a52 + name: Workflow assessment + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - vcffilter2 + - bwa + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2022-12-21' + versions: 2 +- create_time: '2022-12-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 99799eec4497f977 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=99799eec4497f977 + name: Workflow constructed from history 'NGSassignment' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bwa + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2022-12-21' + versions: 3 +- create_time: '2022-12-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3fe3b9a57762841e + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=3fe3b9a57762841e + name: 'Trajectory Analysis: Monocle3 in RStudio' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:trajectory_analysis + - name:single_cell + - name:R + - name:RStudio + tools: + - anndata_inspect + - interactive_tool_rstudio + update_time: '2022-12-19' + versions: 5 +- create_time: '2022-11-22' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Sequencing quality control + edam_topic: [] + id: c2f0decb06f0bb90 + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=c2f0decb06f0bb90 + name: Modular quality control PE + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:IRIS + - name:PE + - name:QC + tools: + - multiqc + - fastp + update_time: '2022-12-12' + versions: 9 +- create_time: '2022-11-18' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Antimicrobial resistance prediction + - Box-Whisker plot plotting + - Structural variation detection + - Scatter plot plotting + edam_topic: [] + id: 3081569659a45b9e + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=3081569659a45b9e + name: Metagenome Antibiotic Resistance Genes on Assemblies + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - nanoplot + - abricate + - filter_tabular + - PlasFlow + - ncbi_acc_download + - isescan + - fasta_merge_files_and_filter_unique_sequences + update_time: '2022-12-09' + versions: 7 +- create_time: '2021-04-01' + creators: + - Guerler + doi: '' + edam_operation: [] + edam_topic: [] + id: a8c8da047f418380 + latest_version: 27 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a8c8da047f418380 + name: Inter-genome interaction prediction + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - spring_model_all + - collection_element_identifiers + - ffindex_dbkit_merge + - __FILTER_FAILED_DATASETS__ + - hhsearch + - rbc_splitfasta + - spring_minz + - ffindex_dbkit_create + update_time: '2022-12-08' + versions: 27 +- create_time: '2021-04-10' + creators: + - Guerler + doi: '' + edam_operation: [] + edam_topic: [] + id: d9fa202d2ff28108 + latest_version: 5 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d9fa202d2ff28108 + name: Intra-genome interaction prediction + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - spring_model_all + - collection_element_identifiers + - __FILTER_FAILED_DATASETS__ + - hhsearch + - rbc_splitfasta + - spring_minz + - ffindex_dbkit_create + update_time: '2022-12-08' + versions: 5 +- create_time: '2022-11-23' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: c2d814f2182c0082 + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=c2d814f2182c0082 + name: Bulk RNASeq to count + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rna_star + - multiqc + - cutadapt + update_time: '2022-12-08' + versions: 7 +- create_time: '2022-12-06' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + edam_topic: [] + id: bb4ecac751a94c79 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=bb4ecac751a94c79 + name: "2es r\xE9sz (3 f\xE1jl kell)" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - limma_voom + update_time: '2022-12-07' + versions: 0 +- create_time: '2022-12-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 29a855d928337f8f + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=29a855d928337f8f + name: elso.resz + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - cutadapt + - multiqc + - featurecounts + - hisat2 + update_time: '2022-12-06' + versions: 0 +- create_time: '2022-12-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 300301c23327f797 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=300301c23327f797 + name: "1es r\xE9sz" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - cutadapt + - multiqc + - featurecounts + - hisat2 + update_time: '2022-12-06' + versions: 0 +- create_time: '2022-12-05' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + edam_topic: [] + id: 47f2c44d79896f08 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=47f2c44d79896f08 + name: Workflow constructed from history '2222 TRCprojekt limmavroom' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - limma_voom + update_time: '2022-12-05' + versions: 0 +- create_time: '2022-12-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3e2718f1ba1a22be + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3e2718f1ba1a22be + name: GTNprocessingMS + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - intens_check + - generic_filter + - normalization + - Multivariate + - Batch_correction + - quality_metrics + update_time: '2022-12-05' + versions: 0 +- create_time: '2021-07-27' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - Coding region prediction + - Validation + - Sequence contamination filtering + - Genome annotation + - Visualisation + - Antimicrobial resistance prediction + - Gene prediction + - Sequencing quality control + - Sequence assembly validation + - Multilocus sequence typing + edam_topic: [] + id: 37da7b42cb063a3a + latest_version: 18 + license: null + link: https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a + name: Bacterial genome assembly - IZSPB + number_of_steps: null + source: https://usegalaxy.eu + tags: + - assembly + - bacterial + - genome + tools: + - fastp + - quast + - abricate + - spades + - mlst + - prokka + - multiqc + - abricate_summary + update_time: '2022-12-03' + versions: 18 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c98a14fcf5998159 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c98a14fcf5998159 + name: RNAseq_PE (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a3da32b6b45da639 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a3da32b6b45da639 + name: RNAseq_SR (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c7a8f7aabc219831 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c7a8f7aabc219831 + name: ChIPseq_SR (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3b8ef7905c902b27 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3b8ef7905c902b27 + name: ATACseq (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 55ead91471bf1008 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=55ead91471bf1008 + name: ChIPseq_PE (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - 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single-cell + - 10x + - transcriptomics + - name:single-cell + tools: + - sort1 + - table_compute + - anndata_manipulate + - anndata_inspect + - scanpy_cluster_reduce_dimension + - cat1 + - tp_easyjoin_tool + - scanpy_plot + - scanpy_regress_variable + - addValue + - scanpy_inspect + update_time: '2022-11-10' + versions: 6 +- create_time: '2022-11-02' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Genome visualisation + - Variant calling + - Phylogenetic tree generation + edam_topic: [] + id: 920aab45ff028ed4 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=920aab45ff028ed4 + name: Microbial Variant Calling (imported from URL) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - variant-analysis + tools: + - jbrowse + - snippy + update_time: '2022-11-09' + versions: 1 +- create_time: '2022-11-08' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Genome assembly + - Sequencing quality control + edam_topic: [] + id: b5ffba506152b1a1 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=b5ffba506152b1a1 + name: Reads-Genomes SR + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - shovill + - fastp + - multiqc + update_time: '2022-11-09' + versions: 4 +- create_time: '2022-11-03' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: fa53b172def3fe75 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=fa53b172def3fe75 + name: RNAseq_PE (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2022-11-03' + versions: 1 +- create_time: '2022-10-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d1d5a6bd6571d47f + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=d1d5a6bd6571d47f + name: SearchGUI/PeptideShaker-MP-Covid + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ident_params + - fasta_cli + - Cut1 + - Remove beginning1 + - Grep1 + - peptide_shaker + - search_gui + - Filter1 + update_time: '2022-10-28' + versions: 2 +- create_time: '2022-10-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c6ca9e6fd28979f8 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c6ca9e6fd28979f8 + name: ChIPseq_SR (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 48f63ef14a12f306 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=48f63ef14a12f306 + name: ATACseq (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-27' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 3aaea772745ca295 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=3aaea772745ca295 + name: 'COVID-19: consensus construction (release v0.4)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9791e8aae12d6e63 + latest_version: 35 + license: null + link: https://usegalaxy.eu/published/workflow?id=9791e8aae12d6e63 + name: Deep Learning for Seabird Behaviour Prediction and Classification + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - keras_model_config + - table_compute + - Remove beginning1 + - column_remove_by_header + - model_prediction + - keras_train_and_eval + - keras_model_builder + - ml_visualization_ex + update_time: '2022-10-24' + versions: 35 +- create_time: '2022-10-20' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 9eb29cc96d8d75c2 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9eb29cc96d8d75c2 + name: 'COVID-19: variation analysis reporting (release v0.3)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-10-20' + versions: 1 +- create_time: '2022-10-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 99ad31bf3970ade4 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=99ad31bf3970ade4 + name: Workflow constructed from history 'Analysing a Human Genome to Identify Pathogenic + Variants' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - bcftools_plugin_split_vep + - snpSift_filter + - snpSift_rmInfo + - ensembl_vep + update_time: '2022-10-18' + versions: 1 +- create_time: '2022-10-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 827e476f6195ac69 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=827e476f6195ac69 + name: Assignment 1 Nino Verwei + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snpEff + - snpSift_filter + - snpSift_rmInfo + update_time: '2022-10-17' + versions: 2 +- create_time: '2022-10-15' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: fed55dc53c5325ff + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=fed55dc53c5325ff + name: Workflow constructed from history 'Galaxy 101 for everyone' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2022-10-15' + versions: 1 +- create_time: '2022-10-15' + creators: [] + doi: '' + edam_operation: + - Sequence visualisation + - Statistical calculation + - SNP annotation + - Genome alignment + - Sequence composition calculation + - Genome indexing + - Read mapping + - Variant calling + - Validation + - Copy number estimation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5ed38d8114bcd6f7 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7 + name: MIRACUM - somatic variant discovery from WES data (hg38 version) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MIRACUM + tools: + - fastqc + - tp_text_file_with_recurring_lines + - trimmomatic + - snpSift_filter + - snpSift_extractFields + - __EXTRACT_DATASET__ + - ensembl_vep + - split_file_to_collection + - collapse_dataset + - __RELABEL_FROM_FILE__ + - tp_replace_in_column + - tp_find_and_replace + - control_freec + - datamash_ops + - varscan_somatic + - Grep1 + - Convert characters1 + - bcftools_plugin_split_vep + - compose_text_param + - samtools_calmd + - multiqc + - __MERGE_COLLECTION__ + - vcfanno + - Add_a_column1 + - tp_replace_in_line + - samtools_rmdup + - __SORTLIST__ + - qualimap_bamqc + - __APPLY_RULES__ + - vcf2maf + - __FILTER_FROM_FILE__ + - param_value_from_file + - __BUILD_LIST__ + - datamash_transpose + - circos + - bwa_mem + - Filter1 + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - tp_easyjoin_tool + - bamleftalign + - samtools_view + update_time: '2022-10-15' + versions: 1 +- create_time: '2022-10-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Validation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4f62794453f65cba + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=4f62794453f65cba + name: "FLUJO DE TRABAJO BIOINFORM\xC1TICO PARA EL AN\xC1LISIS DE DATOS DE SECUENCIACI\xD3\ + N DEL EXOMA PARA EL DIAGN\xD3STICO DE ENFERMEDADES GEN\xC9TICAS MEDIANTE EL USO\ + \ DE LA PLATAFORMA GALAXY" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - samtools_calmd + - trimmomatic + - snpEff_databases + - bg_column_arrange_by_header + - gemini_load + - bamFilter + - samtools_rmdup + - varscan_somatic + - tp_easyjoin_tool + - snpEff + - snpEff_download + - gemini_annotate + - gemini_query + - bamleftalign + - multiqc + - bwa_mem + update_time: '2022-10-14' + versions: 0 +- create_time: '2022-10-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 462582bbc236cb7b + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=462582bbc236cb7b + name: Somatics Variant Calling - HDS + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snpEff + - varscan_somatic + update_time: '2022-10-06' + versions: 1 +- create_time: '2022-09-26' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: a2b386eef5645acd + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=a2b386eef5645acd + name: Cloud computing workshop follow up on Maxquant peptides + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cloud_computing_workshop + - proteomics + tools: + - Cut1 + - Add_a_column1 + - Grep1 + - ggplot2_histogram + - Paste1 + - histogram_rpy + update_time: '2022-10-03' + versions: 5 +- create_time: '2022-09-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Variant calling + - Sequence contamination filtering + - Sequence trimming + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Generation + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: f33b5135ee99e0dc + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc + name: CLIP-Seq-workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - ngsutils_bam_filter + - cutadapt + - htseq_count + - multiqc + - rseqc_bam2wig + - deseq2 + - bwa_mem + update_time: '2022-09-26' + versions: 8 +- create_time: '2022-02-08' + creators: [] + doi: '' + edam_operation: + - Operation + - Genome visualisation + - Genome assembly + - Sequence annotation + - Homology-based gene prediction + - Scaffolding + - Genome annotation + - Transcriptome assembly + - Sequence assembly validation + - Gene prediction + - Ab-initio gene prediction + edam_topic: [] + id: 26ad77bc07a7e512 + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512 + name: Genome gene prediction + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snap_training + - gffread + - jcvi_gff_stats + - fasta-stats + - maker_map_ids + - augustus_training + - jbrowse + - maker + - busco + update_time: '2022-09-26' + versions: 9 +- create_time: '2019-03-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d4603d244cf8ac5b + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=d4603d244cf8ac5b + name: Reads to Peaks + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - deeptools_plot_heatmap + - deeptools_compute_matrix + - trim_galore + - macs2_callpeak + - wig_to_bigWig + - bowtie2 + update_time: '2022-09-23' + versions: 4 +- create_time: '2022-09-19' + creators: + - Mehmet Tekman + doi: '' + edam_operation: + - Annotation + edam_topic: [] + id: a6290cdfa12d34ad + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=a6290cdfa12d34ad + name: Convert from Ensembl to GeneSymbol, summing duplicate genes + number_of_steps: null + source: https://usegalaxy.eu + tags: + - gene + - convert + tools: + - sort1 + - table_compute + - annotatemyids + - tp_cut_tool + - tp_easyjoin_tool + - tp_sed_tool + - tp_awk_tool + update_time: '2022-09-19' + versions: 7 +- create_time: '2022-09-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a3a7c1853ae7047b + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=a3a7c1853ae7047b + name: Monocle3 workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:trajectory_analysis + - name:transcriptomics + - name:scRNA-seq + tools: + - monocle3_partition + - monocle3_reduceDim + - monocle3_orderCells + - monocle3_plotCells + - monocle3_topmarkers + - monocle3_learnGraph + - monocle3_diffExp + - monocle3_create + - monocle3_preprocess + update_time: '2022-09-19' + versions: 3 +- create_time: '2022-09-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9a657909d6191203 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=9a657909d6191203 + name: AnnData object to Monocle input files + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:trajectory_analysis + - name:transcriptomics + - name:scRNA-seq + - name:AnnData2Monocle + tools: + - Cut1 + - anndata_inspect + - join1 + - regexColumn1 + - tp_cut_tool + - datamash_transpose + - Filter1 + update_time: '2022-09-19' + versions: 4 +- create_time: '2022-08-12' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 4b9459829b45ec67 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=4b9459829b45ec67 + name: galaxy-101visible=true + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - __DATA_FETCH__ + - tp_head_tool + - comp1 + update_time: '2022-09-18' + versions: 0 +- create_time: '2022-09-12' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: ccec1752fcac5e3f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=ccec1752fcac5e3f + name: Fastq_filter_and_QC 'SB_day1_history' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2022-09-12' + versions: 1 +- create_time: '2022-09-02' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 9a7d8552f5774fbd + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=9a7d8552f5774fbd + name: CS3_Filter, Plot and Explore Single-cell RNA-seq Data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:training + - name:single-cell + tools: + - anndata_manipulate + - scanpy_find_cluster + - scanpy_scale_data + - anndata_inspect + - scanpy_compute_graph + - scanpy_find_markers + - scanpy_plot_embed + - Cut1 + - scanpy_normalise_data + - join1 + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_plot + - anndata_ops + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2022-09-05' + versions: 7 +- create_time: '2022-08-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ea102016a86c3eff + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=ea102016a86c3eff + name: CS2_Combining datasets after pre-processing + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:training + - name:single-cell + tools: + - anndata_manipulate + - anndata_inspect + - scanpy_read_10x + - Cut1 + - tp_replace_in_column + - Paste1 + - anndata_ops + - retrieve_scxa + update_time: '2022-09-05' + versions: 5 +- create_time: '2022-08-28' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: df926c5ab8d27192 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192 + name: Metaproteomics_GTN_IMSC2022_Aug28 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2022-08-28' + versions: 2 +- create_time: '2022-08-27' + creators: + - Wendi Bacon + doi: '' + edam_operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + edam_topic: [] + id: 9ed36a6849fa2014 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=9ed36a6849fa2014 + name: CS1_Generating a single cell matrix using Alevin + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:single-cell + - name:training + tools: + - Cut1 + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - join1 + - dropletutils_read_10x + - sceasy_convert + - _dropletBarcodePlot + - dropletutils_empty_drops + update_time: '2022-08-27' + versions: 1 +- create_time: '2022-08-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 1d1092f57e418c57 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=1d1092f57e418c57 + name: NCBI DNA seq_DEMO 'BBL735_Lab3_(DNA_fastQC)_AT' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - cutadapt + update_time: '2022-08-23' + versions: 2 +- create_time: '2022-08-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 21c8ee4af52a3931 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=21c8ee4af52a3931 + name: NCBI_DNA_RNA Seq 'BBL735_Lab3_(DNA_fastQC)_AT' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - cutadapt + update_time: '2022-08-23' + versions: 1 +- create_time: '2022-08-23' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 519e0ffdfd1790bc + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=519e0ffdfd1790bc + name: FASTQC_Quality Control 'BBL735_Lab3(Fastqc)_AT' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastqe + - cutadapt + - multiqc + update_time: '2022-08-23' + versions: 2 +- create_time: '2022-08-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0c7c2a4f801efc19 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=0c7c2a4f801efc19 + name: Multimodal Omics Data Integration with Muon (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mudata_import + - compare_annotations + - mofa + - cluster_mofa_embeddings_with_mudata + - assign_cell_type_labels_mudata + - rank_genes_and_peaks_muon + - visualise_markers_mudata + update_time: '2022-08-22' + versions: 0 +- create_time: '2022-08-21' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 5fb6cb6c80a5c62f + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=5fb6cb6c80a5c62f + name: Workflow constructed from history 'BBL735_AS_Lab2' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2022-08-21' + versions: 0 +- create_time: '2022-08-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9bafb4701a4c0426 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=9bafb4701a4c0426 + name: Workflow constructed from history 'BBL735_AS_Lab2' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - csv_to_tabular + - tp_sorted_uniq + - Remove beginning1 + - Cut1 + update_time: '2022-08-21' + versions: 0 +- create_time: '2022-08-16' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 9edd9ccffe6f4c59 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=9edd9ccffe6f4c59 + name: Find exons with highest number of features + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2022-08-21' + versions: 0 +- create_time: '2022-08-21' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 321ea55011f1248f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=321ea55011f1248f + name: Exploring Iris dataset with statistics and scatterplots + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2022-08-21' + versions: 1 +- create_time: '2022-08-19' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 6f4bbed7a320dc2f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6f4bbed7a320dc2f + name: Exploring Iris dataset with statistics and scatterplots_BBL735_LAB2_AT + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - ggplot2_point + - bg_uniq + update_time: '2022-08-21' + versions: 1 +- create_time: '2022-08-19' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 516b4d4146e4af66 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=516b4d4146e4af66 + name: Dimond__BBL735_Lab2_Test_dimond_AT' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - ggplot2_point + - bg_uniq + update_time: '2022-08-21' + versions: 3 +- create_time: '2022-08-12' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 6dbc84168feea337 + latest_version: 6 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6dbc84168feea337 + name: FastQC and MultiQC on Paired data + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - multiqc + - __MERGE_COLLECTION__ + - __UNZIP_COLLECTION__ + update_time: '2022-08-19' + versions: 6 +- create_time: '2022-08-13' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 4f9f050e34747d51 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=4f9f050e34747d51 + name: What are the differences between the Iris species? + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - ggplot2_point + update_time: '2022-08-18' + versions: 1 +- create_time: '2022-08-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1b72af1870c540d6 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=1b72af1870c540d6 + name: How can I do basic data manipulation in Galaxy? Which tools are available + to convert, reformat, filter, sort etc my text-based data? + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - Count1 + - Remove beginning1 + - Cut1 + - column_remove_by_header + - datamash_ops + - tabular_to_csv + - regexColumn1 + - join1 + - cat1 + - tp_sorted_uniq + - wc_gnu + - Filter1 + update_time: '2022-08-18' + versions: 0 +- create_time: '2022-08-10' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 96b75a7373a58aae + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=96b75a7373a58aae + name: which exon has the highest number of SNPs on human chromosome 22? + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - bedtools_intersectbed + - datamash_ops + - tp_head_tool + - tp_sort_header_tool + update_time: '2022-08-10' + versions: 2 +- create_time: '2022-08-07' + creators: [] + doi: '' + edam_operation: + - Variant calling + - RNA-Seq analysis + - Transcriptome assembly + - Statistical calculation + - Sequence alignment + - Sequence annotation + edam_topic: [] + id: 3a8150c81b90a3a7 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7 + name: 'IMSC2022 Proteogenomics 1: Database Creation' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - filter_tabular + - tp_cat + - stringtie + - fasta2tab + - query_tabular + - regexColumn1 + - fasta_merge_files_and_filter_unique_sequences + - bed_to_protein_map + - tp_replace_in_column + - hisat2 + - gffcompare + - tab2fasta + - gffcompare_to_bed + - custom_pro_db + - sqlite_to_tabular + - translate_bed + - freebayes + update_time: '2022-08-08' + versions: 0 +- create_time: '2022-07-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 39dd6365ff076dc4 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=39dd6365ff076dc4 + name: music_compare + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - music_compare + - music_construct_eset + - Cut1 + - tp_split_on_column + update_time: '2022-08-05' + versions: 2 +- create_time: '2021-08-09' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 6d06bd22f206e176 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=6d06bd22f206e176 + name: 16S rDNA microbial analisys + MUSCLE mothur + number_of_steps: null + source: https://usegalaxy.eu + tags: + - 16S + - mothur + - microbial + - microbiome + - OTU + - Cluster + - Rarefaction + tools: + - muscle + - mothur_chimera_uchime + - mothur_remove_seqs + - mothur_dist_seqs + - mothur_cluster + - mothur_get_oturep + - mothur_rarefaction_single + - mothur_unique_seqs + update_time: '2022-07-29' + versions: 8 +- create_time: '2021-06-11' + creators: [] + doi: '' + edam_operation: + - Peptide database search + - Visualisation + - Conversion + - Prediction and recognition + edam_topic: [] + id: 8a85663218676b59 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=8a85663218676b59 + name: COVID workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:COVID + tools: + - Remove beginning1 + - Cut1 + - query_tabular + - pepquery + - mz_to_sqlite + - Grouping1 + - Grep1 + - peptide_shaker + - unipept + - search_gui + - Filter1 + update_time: '2022-07-15' + versions: 3 +- create_time: '2022-07-13' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - RNA-Seq analysis + - Transcriptome assembly + - Generation + - Sequence alignment + edam_topic: [] + id: 1cd85fe90839c10d + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=1cd85fe90839c10d + name: Benchmarking DNA Cloud Costs + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - stringtie + - bwa_mem + - bwa + - bowtie2 + - hisat2 + update_time: '2022-07-13' + versions: 0 +- create_time: '2022-07-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - RNA-Seq analysis + - Pathway or network analysis + - Sequencing quality control + edam_topic: [] + id: 65aed668233d5f73 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=65aed668233d5f73 + name: Salmon + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - tximport + - fasterq_dump + - salmon + update_time: '2022-07-12' + versions: 1 +- create_time: '2022-07-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 79eb28066236e836 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=79eb28066236e836 + name: COVID-VERIFICATION-WORKFLOW + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_blastp_wrapper + - Cut1 + - collapse_dataset + - tp_cat + - query_tabular + - pepquery + - Grouping1 + - tab2fasta + - Filter1 + update_time: '2022-07-03' + versions: 1 +- create_time: '2022-07-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Heat map generation + - Filtering + - Standardisation and normalisation + - Protein quantification + - Peptide database search + - Visualisation + - Imputation + - Conversion + - Clustering + - Principal component plotting + edam_topic: [] + id: eb54512829d8509c + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=eb54512829d8509c + name: COVID_DISCOVERY-workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ident_params + - maxquant + - fasta_cli + - filter_tabular + - Cut1 + - tp_cat + - query_tabular + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - mz_to_sqlite + - Grouping1 + - Grep1 + - search_gui + - peptide_shaker + - dbbuilder + - msconvert + - Filter1 + update_time: '2022-07-03' + versions: 1 +- create_time: '2022-06-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6201ec86d380aef1 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=6201ec86d380aef1 + name: COVID-VERIFICATION-WORKFLOW + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_blastp_wrapper + - Cut1 + - collapse_dataset + - tp_cat + - query_tabular + - pepquery + - Grouping1 + - tab2fasta + - Filter1 + update_time: '2022-07-03' + versions: 6 +- create_time: '2022-06-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Heat map generation + - Filtering + - Standardisation and normalisation + - Protein quantification + - Peptide database search + - Visualisation + - Imputation + - Conversion + - Clustering + - Principal component plotting + edam_topic: [] + id: 41e9882300fa2386 + latest_version: 10 + license: null + link: https://usegalaxy.eu/published/workflow?id=41e9882300fa2386 + name: COVID-DISCOVERY-WORKFLOW + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ident_params + - maxquant + - fasta_cli + - filter_tabular + - Cut1 + - tp_cat + - query_tabular + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - mz_to_sqlite + - Grouping1 + - Grep1 + - search_gui + - peptide_shaker + - dbbuilder + - msconvert + - Filter1 + update_time: '2022-07-03' + versions: 10 +- create_time: '2022-06-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a824cfdee241177f + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=a824cfdee241177f + name: FragPipe Accession Numbers of PepQuery Verified Peptides + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - collapse_dataset + - query_tabular + - Grouping1 + update_time: '2022-06-29' + versions: 4 +- create_time: '2022-06-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b06f5729d6d68794 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=b06f5729d6d68794 + name: MaxQuant Accession Numbers of PepQuery Verified Peptides + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - collapse_dataset + - query_tabular + - Grouping1 + update_time: '2022-06-29' + versions: 3 +- create_time: '2022-06-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b6bb29169160a713 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=b6bb29169160a713 + name: SGPS Accession Numbers of PepQuery Verified Peptides + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - collapse_dataset + - query_tabular + - Grouping1 + update_time: '2022-06-29' + versions: 3 +- create_time: '2022-06-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d95a3349f38792fc + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=d95a3349f38792fc + name: PEPQUERY VERIFICATION WORKFLOW + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - collapse_dataset + - pepquery + - Grouping1 + - Filter1 + update_time: '2022-06-29' + versions: 1 +- create_time: '2022-06-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome alignment + - Sequence composition calculation + - Genome indexing + - Read mapping + - Variant calling + - Validation + - Copy number estimation + - Generation + - Sequencing quality control + - Sequence alignment + - Sequence visualisation + edam_topic: [] + id: b1d1694b95ed10e1 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=b1d1694b95ed10e1 + name: ' Control-FREEC/MIRACUM - somatic variant discovery from WES data' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MIRACUM + tools: + - fastqc + - control_freec + - tp_text_file_with_recurring_lines + - trimmomatic + - samtools_calmd + - samtools_view + - tp_replace_in_line + - samtools_rmdup + - __RELABEL_FROM_FILE__ + - Grep1 + - bamleftalign + - multiqc + - __BUILD_LIST__ + - circos + - bwa_mem + update_time: '2022-06-28' + versions: 0 +- create_time: '2022-06-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c02ff9e97ce796c6 + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=c02ff9e97ce796c6 + name: PEPQUERY VERIFICATION WORKFLOW FOR SGPS + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - collapse_dataset + - query_tabular + - pepquery + - Grouping1 + - Filter1 + update_time: '2022-06-24' + versions: 11 +- create_time: '2022-06-16' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: c2c7f1815c411bfb + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=c2c7f1815c411bfb + name: Quality Evaluation (release v0.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - meryl + - genomescope + update_time: '2022-06-16' + versions: 1 +- create_time: '2022-06-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 99022559adf01c4a + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=99022559adf01c4a + name: Workflow constructed from history 'WES_chrm22' (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - pileup_parser + - picard_SortSam + - samtools_idxstats + - freebayes + - sam_pileup + - snpEff + - samtools_flagstat + - Filter1 + - bamtools + - bwa_mem + update_time: '2022-06-13' + versions: 0 +- create_time: '2022-06-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 36a4646959829018 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=36a4646959829018 + name: Workflow constructed from history 'WES_chrm22' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - pileup_parser + - picard_SortSam + - samtools_idxstats + - freebayes + - sam_pileup + - snpEff + - samtools_flagstat + - Filter1 + - bamtools + - bwa_mem + update_time: '2022-06-13' + versions: 0 +- create_time: '2022-01-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ad4b347f9b68e127 + latest_version: 30 + license: null + link: https://usegalaxy.eu/published/workflow?id=ad4b347f9b68e127 + name: CUT_and_RUN_TM + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CUT_and_RUN + tools: + - fastqc + - bedtools_bamtobed + - Extract genomic DNA 1 + - trim_galore + - bamFilter + - meme_chip + - bedtools_intersectbed + - __FLATTEN__ + - __APPLY_RULES__ + - macs2_callpeak + - picard_MarkDuplicates + - macs2_predictd + - bowtie2 + - pe_histogram + update_time: '2022-06-13' + versions: 30 +- create_time: '2021-12-09' + creators: [] + doi: '' + edam_operation: + - Genome annotation + - Sequence visualisation + edam_topic: [] + id: 2d0400b5d05c6c10 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10 + name: MITOS annotation and CIRCOS plot + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - circos_interval_to_tile + - Cut1 + - Add_a_column1 + - tp_cat + - circos_interval_to_text + - tp_grep_tool + - tp_replace_in_column + - mitos2 + - circos + - fasta_compute_length + update_time: '2022-06-10' + versions: 0 +- create_time: '2022-04-04' + creators: [] + doi: '' + edam_operation: + - Validation + - Alignment + - Genome annotation + - Visualisation + edam_topic: [] + id: 0a692a2e643b9e1a + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=0a692a2e643b9e1a + name: Preprocessing_scPipe + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scpipe + update_time: '2022-06-10' + versions: 6 +- create_time: '2022-04-08' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: b3cf397fd4d1bea8 + latest_version: 20 + license: null + link: https://usegalaxy.eu/published/workflow?id=b3cf397fd4d1bea8 + name: downstream_scanpy + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_find_cluster + - scanpy_scale_data + - scanpy_plot_embed + - scanpy_compute_graph + - scanpy_normalise_data + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_remove_confounders + - scanpy_plot + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2022-06-10' + versions: 20 +- create_time: '2022-05-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6afc245029ce5008 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=6afc245029ce5008 + name: Xarray_Map_Plotting_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - xarray_metadata_info + - cdo_operations + - xarray_mapplot + - graphicsmagick_image_montage + - xarray_coords_info + update_time: '2022-06-07' + versions: 2 +- create_time: '2022-06-07' + creators: + - Soumya Jha + doi: '' + edam_operation: [] + edam_topic: [] + id: d94460f342b70eb3 + latest_version: 3 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=d94460f342b70eb3 + name: Xarray_Map_Plotting_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ecology + - climate + tools: + - xarray_metadata_info + - xarray_coords_info + - cdo_operations + - xarray_mapplot + update_time: '2022-06-07' + versions: 3 +- create_time: '2022-03-30' + creators: [] + doi: '' + edam_operation: + - Sequence comparison + - Sequence alignment analysis + - Sequence similarity search + edam_topic: [] + id: e423c80058601e78 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=e423c80058601e78 + name: 3.Data Parallel running + number_of_steps: null + source: https://usegalaxy.eu + tags: + - '3.24' + tools: + - fasplit + - collapse_dataset + - fastq_to_fasta_python + - fastq_paired_end_interlacer + - bg_sortmerna + - fastq_combiner + update_time: '2022-06-06' + versions: 3 +- create_time: '2022-03-30' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + - Phylogenetic inference + - Phylogenetic tree visualisation + - Visualisation + - Conversion + - Phylogenetic tree analysis + - Nucleic acid sequence analysis + - Phylogenetic tree editing + edam_topic: [] + id: 4f21205e71cabd37 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37 + name: 2.Community Profile + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - taxonomy_krona_chart + - Cut1 + - export2graphlan + - graphlan + - graphlan_annotate + - metaphlan + update_time: '2022-06-06' + versions: 3 +- create_time: '2022-03-30' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 3183c2abca463bb4 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=3183c2abca463bb4 + name: 1.Preprocessing + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - multiqc + - cutadapt + update_time: '2022-06-06' + versions: 4 +- create_time: '2022-05-13' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Data handling + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 7783eeebfa264bf5 + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=7783eeebfa264bf5 + name: 16S rRNA oral microbiata + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mothur_summary_seqs + - mothur_make_group + - mothur_filter_seqs + - fasterq_dump + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_cluster_split + - mothur_merge_files + - mothur_make_shared + - mothur_unique_seqs + - mothur_align_seqs + - mothur_classify_otu + - mothur_classify_seqs + - mothur_pre_cluster + update_time: '2022-05-29' + versions: 7 +- create_time: '2022-05-26' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Data handling + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 6efd80daabf518bf + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6efd80daabf518bf + name: 16S rRNA classification with mothur + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mothur_summary_seqs + - mothur_filter_seqs + - fasterq_dump + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_cluster_split + - mothur_make_shared + - mothur_unique_seqs + - mothur_align_seqs + - mothur_classify_otu + - mothur_classify_seqs + - mothur_pre_cluster + update_time: '2022-05-29' + versions: 1 +- create_time: '2022-03-30' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree analysis + - Nucleic acid sequence analysis + - Species frequency estimation + edam_topic: [] + id: 21a17d6c473a88c0 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0 + name: 6.merged_samples_functional_analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - merge_metaphlan_tables + - Cut1 + - combine_metaphlan2_humann2 + - humann_join_tables + - Grep1 + - humann_unpack_pathways + - humann_rename_table + - humann_regroup_table + update_time: '2022-05-24' + versions: 5 +- create_time: '2022-05-10' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + - Phylogenetic inference + - Phylogenetic tree visualisation + - Conversion + - Phylogenetic tree editing + edam_topic: [] + id: b5f848dc8e96663c + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c + name: 5.taxon_viz + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - metaphlan2krona + - Cut1 + - export2graphlan + - krona-text + - graphlan + - graphlan_annotate + update_time: '2022-05-24' + versions: 4 +- create_time: '2022-05-10' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Taxonomic classification + - Species frequency estimation + edam_topic: [] + id: 3118d383c81cf805 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=3118d383c81cf805 + name: 4 Functional Information + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - humann_split_stratified_table + - Cut1 + - humann_unpack_pathways + - Grep1 + - humann_renorm_table + - humann + - combine_metaphlan2_humann2 + - humann_rename_table + - humann_regroup_table + update_time: '2022-05-24' + versions: 1 +- create_time: '2022-05-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Phylogenetic analysis + - Sequence alignment analysis + - Phylogenetic inference + - Primer removal + - Species frequency estimation + - Sequence similarity search + - Sequencing quality control + - Taxonomic classification + - Sequence composition calculation + - Sequence comparison + - Phylogenetic tree visualisation + - Validation + - Sequence trimming + - Visualisation + - Phylogenetic tree analysis + - Conversion + - Read pre-processing + - Nucleic acid sequence analysis + - Phylogenetic tree editing + edam_topic: [] + id: 4d32b1b3ac0a7161 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161 + name: metatranscriptmoics + number_of_steps: null + source: https://usegalaxy.eu + tags: + - xy + tools: + - fastqc + - humann_split_stratified_table + - fasplit + - collapse_dataset + - graphlan_annotate + - humann_regroup_table + - metaphlan + - taxonomy_krona_chart + - fastq_to_fasta_python + - cutadapt + - Grep1 + - graphlan + - multiqc + - fastq_combiner + - humann_unpack_pathways + - export2graphlan + - fastq_paired_end_interlacer + - humann + - combine_metaphlan2_humann2 + - Cut1 + - humann_renorm_table + - bg_sortmerna + - humann_rename_table + update_time: '2022-05-24' + versions: 1 +- create_time: '2022-05-24' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic inference + - Species frequency estimation + - Phylogenetic tree visualisation + - Phylogenetic tree analysis + - Conversion + - Nucleic acid sequence analysis + - Phylogenetic tree editing + edam_topic: [] + id: 713a5485e2007f90 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=713a5485e2007f90 + name: merged results + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - metaphlan2krona + - merge_metaphlan_tables + - Cut1 + - export2graphlan + - combine_metaphlan2_humann2 + - krona-text + - humann_join_tables + - Grep1 + - graphlan + - humann_unpack_pathways + - humann_rename_table + - graphlan_annotate + - humann_regroup_table + update_time: '2022-05-24' + versions: 2 +- create_time: '2022-05-09' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: da3a6d229e422dde + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=da3a6d229e422dde + name: Workflow 'Galaxy introduction' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2022-05-18' + versions: 1 +- create_time: '2022-05-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a0f1959a9f4533f7 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7 + name: Downstream_Seurat_rdata + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seurat_filter_cells + - seurat_find_variable_genes + - seurat_run_pca + - seurat_find_neighbours + - sceasy_convert + - seurat_find_clusters + - seurat_scale_data + - seurat_find_markers + - seurat_dim_plot + - seurat_run_tsne + - seurat_normalise_data + update_time: '2022-05-16' + versions: 3 +- create_time: '2022-04-04' + creators: [] + doi: '' + edam_operation: + - Community profiling + - Read summarisation + - Data handling + - Sequence alignment analysis + - RNA-Seq quantification + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: af7c349497a75314 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=af7c349497a75314 + name: Preprocessing_UMI_STAR + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - __UNZIP_COLLECTION__ + - umi_tools_extract + - bamFilter + - umi_tools_count + - rna_star + - dropletutils + - featurecounts + update_time: '2022-05-16' + versions: 3 +- create_time: '2022-04-04' + creators: [] + doi: '' + edam_operation: + - Community profiling + - Sequence alignment + - Loading + edam_topic: [] + id: e7494f29c8672f34 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=e7494f29c8672f34 + name: Preprocessing_STARSolo + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rna_starsolo + - dropletutils + update_time: '2022-05-16' + versions: 8 +- create_time: '2022-04-05' + creators: [] + doi: '' + edam_operation: + - Community profiling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Loading + edam_topic: [] + id: 83ae28e23099a3f6 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6 + name: Preprocessing_Alevin + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - __UNZIP_COLLECTION__ + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - dropletutils + update_time: '2022-05-16' + versions: 3 +- create_time: '2022-02-12' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 37b04b02ec08e84f + latest_version: 2 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=37b04b02ec08e84f + name: 'COVID-19: variation analysis reporting - iwc version 0.2' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-05-13' + versions: 2 +- create_time: '2022-05-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4f0f3b911b4e4921 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921 + name: Workflow2 constructed from history 'Workflow Extraction' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - xarray_metadata_info + - cdo_operations + - xarray_mapplot + - xarray_netcdf2netcdf + - graphicsmagick_image_montage + - xarray_coords_info + update_time: '2022-05-03' + versions: 0 +- create_time: '2022-04-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9a0275211e74698a + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=9a0275211e74698a + name: EBI SC Expression Atlas Release 19 Analysis Pipeline v0.2.5 (Scanpy 1.8.1 + - plate) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_read_10x + - scanpy_compute_graph + - __FILTER_FAILED_DATASETS__ + - scanpy_normalise_data + - join1 + - scanpy_filter_cells + - scanpy_find_variable_genes + - Remove beginning1 + - scanpy_find_markers + - __MERGE_COLLECTION__ + - scanpy_run_pca + - tp_replace_in_line + - scanpy_run_tsne + - scanpy_run_umap + - anndata_ops + - __BUILD_LIST__ + - scanpy_find_cluster + - Cut1 + - bg_column_arrange_by_header + - scanpy_filter_genes + - scanpy_integrate_harmony + - scanpy_parameter_iterator + update_time: '2022-04-27' + versions: 2 +- create_time: '2021-07-27' + creators: + - BMCV Group, Heidelberg University + doi: '' + edam_operation: + - Image analysis + edam_topic: [] + id: ffa80e0637d079f2 + latest_version: 21 + license: null + link: https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2 + name: Capturing mitoflashes + number_of_steps: null + source: https://usegalaxy.eu + tags: + - mito-flash + - mitochondrion_tracking + tools: + - ip_curve_fitting + - ip_points_association_nn + - ip_spot_detection_2d + update_time: '2022-04-25' + versions: 21 +- create_time: '2022-04-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b4bfcbf8acee9cc3 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3 + name: Plotting of Geographical Map using climate Data + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - xarray_metadata_info + - cdo_operations + - xarray_mapplot + - xarray_netcdf2netcdf + - graphicsmagick_image_montage + - xarray_coords_info + - xarray_select + update_time: '2022-04-20' + versions: 4 +- create_time: '2022-04-08' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - RNA-Seq quantification + - Sequence alignment + - Read summarisation + - Sequence annotation + edam_topic: [] + id: e8202b7b6338005d + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=e8202b7b6338005d + name: Phage RNA-Seq + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - stringtie + - gffcompare + - stringtie_merge + - featurecounts + - deseq2 + - hisat2 + update_time: '2022-04-13' + versions: 3 +- create_time: '2022-04-11' + creators: + - smehta + doi: '' + edam_operation: + - Peptide database search + - Conversion + edam_topic: [] + id: 6e5f0d05c91876c2 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2 + name: Omicron, Delta and Gamma Covid strains discovery workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - filter_tabular + - Cut1 + - collapse_dataset + - query_tabular + - fasta2tab + - pepquery + - fasta_merge_files_and_filter_unique_sequences + - mz_to_sqlite + - Grouping1 + - Grep1 + - peptide_shaker + - dbbuilder + - search_gui + - Filter1 + update_time: '2022-04-11' + versions: 1 +- create_time: '2022-04-11' + creators: + - smehta + doi: '' + edam_operation: + - Peptide database search + - Conversion + edam_topic: [] + id: 03e52c8c71710cae + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae + name: Omicron-COVIDstrains-discovery workflow-SGPS + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid19 + - name:oldsgps + tools: + - filter_tabular + - Cut1 + - collapse_dataset + - query_tabular + - fasta2tab + - pepquery + - fasta_merge_files_and_filter_unique_sequences + - mz_to_sqlite + - Grouping1 + - peptide_shaker + - dbbuilder + - search_gui + - Filter1 + update_time: '2022-04-11' + versions: 2 +- create_time: '2022-03-31' + creators: + - smehta + doi: '' + edam_operation: + - Peptide database search + - Conversion + edam_topic: [] + id: 9a8b5e99ca9500e3 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3 + name: Omicron-COVIDstrains-discovery workflow (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid19 + tools: + - ident_params + - filter_tabular + - Cut1 + - collapse_dataset + - query_tabular + - fasta2tab + - pepquery + - fasta_merge_files_and_filter_unique_sequences + - mz_to_sqlite + - Grouping1 + - peptide_shaker + - dbbuilder + - search_gui + - Filter1 + update_time: '2022-04-11' + versions: 1 +- create_time: '2022-04-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5a16af00bf8bf57b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=5a16af00bf8bf57b + name: Workflow constructed from history 'SNP FINAL ASSIGNMENT' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - Cut1 + - bamFilter + - vcffilter2 + - vcf2tsv + - bamleftalign + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2022-04-10' + versions: 0 +- create_time: '2022-04-08' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 8172bf190ce30036 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=8172bf190ce30036 + name: Exploring Iris Dataset with Statistics and Scatterplots + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2022-04-08' + versions: 0 +- create_time: '2022-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 785433e42d82be65 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=785433e42d82be65 + name: Preprocessing Workflow Maren + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cardinal_preprocessing + - cardinal_filtering + - cardinal_data_exporter + update_time: '2022-04-08' + versions: 1 +- create_time: '2022-04-06' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Read mapping + - Variant calling + - Phylogenetic tree generation + edam_topic: [] + id: 464b642261ed7452 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=464b642261ed7452 + name: Workflow constructed from history 'WT' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snippy + - bowtie2 + update_time: '2022-04-06' + versions: 0 +- create_time: '2022-03-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a6a36943accc9b7d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a6a36943accc9b7d + name: ExonSNP-2022 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - tp_sort_header_tool + - Add_a_column1 + - gops_join_1 + - Grouping1 + update_time: '2022-03-31' + versions: 1 +- create_time: '2022-03-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7463b26aab6a965d + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d + name: Peptide And Protein ID Tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: + - proteomics + tools: + - ident_params + - fasta_cli + - PeakPickerHiRes + - FileConverter + - Grep1 + - peptide_shaker + - search_gui + update_time: '2022-03-31' + versions: 6 +- create_time: '2022-03-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 82ef590b5821805d + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=82ef590b5821805d + name: Workflow AM + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - join1 + - ggplot2_pca + - tp_replace_in_column + - hisat2 + - Remove beginning1 + - stringtie + - ggplot2_heatmap2 + - cat1 + - multiqc + - deseq2 + - sort1 + - table_compute + - Add_a_column1 + - tp_cat + - volcanoplot + - ggplot2_point + - addValue + - tp_multijoin_tool + - Filter1 + - Cut1 + - subtract_query1 + update_time: '2022-03-28' + versions: 3 +- create_time: '2022-03-27' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - Coding region prediction + - Scaffolding + - Differential gene expression analysis + - Genome annotation + - Transcriptome assembly + - Sequence clustering + - Antimicrobial resistance prediction + - Gene prediction + - Sequence assembly validation + edam_topic: [] + id: 6984990d0ac2e1e6 + latest_version: 5 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6 + name: 03_Annotation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - prokka + - antismash + - abricate + - busco + update_time: '2022-03-28' + versions: 5 +- create_time: '2022-03-27' + creators: [] + doi: '' + edam_operation: + - Sequencing quality control + - Base-calling + - Genome assembly + - De-novo assembly + - Filtering + - Variant calling + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: 86cf02cc0868d238 + latest_version: 3 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238 + name: 02_Assembly + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - nanoplot + - medaka_consensus_pipeline + - bandage_info + - flye + - filtlong + - porechop + - bandage_image + update_time: '2022-03-28' + versions: 3 +- create_time: '2022-03-27' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + - Box-Whisker plot plotting + - Scatter plot plotting + edam_topic: [] + id: 0bafeb17c21ebc9c + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c + name: 01_Raw_QC + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - taxonomy_krona_chart + - kraken2 + - nanoplot + - Kraken2Tax + update_time: '2022-03-27' + versions: 2 +- create_time: '2022-03-21' + creators: [] + doi: '' + edam_operation: + - De-novo assembly + - Genome alignment + - Coding region prediction + - Variant calling + - Differential gene expression analysis + - Genome annotation + - Antimicrobial resistance prediction + - Box-Whisker plot plotting + - Sequence clustering + - Filtering + - Sequence assembly + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + - Base-calling + - Genome assembly + - Scaffolding + - Transcriptome assembly + - Cross-assembly + - Mapping assembly + - Gene prediction + - Sequence similarity search + - Scatter plot plotting + edam_topic: [] + id: bf48b0eb15e8ff75 + latest_version: 8 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75 + name: 27255_matinnu + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastani + - nanoplot + - abricate + - medaka_consensus_pipeline + - flye + - filtlong + - prokka + - antismash + - porechop + - bandage_image + - busco + update_time: '2022-03-25' + versions: 8 +- create_time: '2022-03-21' + creators: + - Poorani + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Variant calling + - Phylogenetic tree generation + edam_topic: [] + id: a183da6b56cd1d60 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60 + name: Snippy and TB Variant Filter ACE Uganda Winter 2022 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snippy + - tb_variant_filter + update_time: '2022-03-21' + versions: 4 +- create_time: '2021-11-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome alignment + - Sequence composition calculation + - Genome indexing + - Read mapping + - Variant calling + - Validation + - Copy number estimation + - Generation + - Sequencing quality control + - Sequence alignment + - Sequence visualisation + edam_topic: [] + id: 6ed1016dfdf9f928 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928 + name: MIRACUM - somatic variant discovery from WES data (imported from uploaded + file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MIRACUM + tools: + - fastqc + - tp_text_file_with_recurring_lines + - trimmomatic + - __EXTRACT_DATASET__ + - split_file_to_collection + - collapse_dataset + - __RELABEL_FROM_FILE__ + - tp_replace_in_column + - tp_find_and_replace + - control_freec + - datamash_ops + - varscan_somatic + - Grep1 + - Convert characters1 + - gemini_annotate + - compose_text_param + - samtools_calmd + - multiqc + - __MERGE_COLLECTION__ + - Add_a_column1 + - tp_replace_in_line + - samtools_rmdup + - __SORTLIST__ + - qualimap_bamqc + - gemini_query + - __APPLY_RULES__ + - __FILTER_FROM_FILE__ + - snpEff + - param_value_from_file + - __BUILD_LIST__ + - datamash_transpose + - circos + - bwa_mem + - Filter1 + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - gemini_load + - tp_easyjoin_tool + - bamleftalign + - samtools_view + update_time: '2022-03-18' + versions: 4 +- create_time: '2022-03-18' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 843c10c447496280 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=843c10c447496280 + name: MMGBSA calculations with GROMACS (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: abd1cb3457338eb5 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5 + name: MMGBSA calculations with GROMACS (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 1b10ece62e745125 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1b10ece62e745125 + name: dcTMD calculations with GROMACS (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_text_file_with_recurring_lines + - split_file_to_collection + - add_line_to_file + - tp_cat + - gmx_sim + - biomd_neqgamma + - gmx_solvate + - tp_sed_tool + - gmx_makendx + - compose_text_param + - ctb_online_data_fetch + - param_value_from_file + - gmx_em + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4c75ab0be3c56494 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494 + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9feebfc6c34da287 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287 + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 74f19aff1b9cdd6b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: e0dddc2579c3614e + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=e0dddc2579c3614e + name: Create GRO and TOP complex files (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ambertools_acpype + - Cut1 + - ctb_rdkit_descriptors + - gmx_setup + - tp_grep_tool + - gmx_merge_topology_files + - param_value_from_file + - ambertools_antechamber + - openbabel_compound_convert + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 84c95f31896213fd + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=84c95f31896213fd + name: Create GRO and TOP complex files (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ambertools_acpype + - Cut1 + - ctb_rdkit_descriptors + - gmx_setup + - tp_grep_tool + - gmx_merge_topology_files + - param_value_from_file + - ambertools_antechamber + - openbabel_compound_convert + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 20592f292c205954 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=20592f292c205954 + name: 'COVID-19: variation analysis reporting (release v0.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 88f5cef7e4146520 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=88f5cef7e4146520 + name: 'COVID-19: variation analysis reporting (release v0.1.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 27fca972f1d1a312 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=27fca972f1d1a312 + name: 'COVID-19: variation analysis reporting (release v0.1.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 0c94260298199d8b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0c94260298199d8b + name: 'COVID-19: variation analysis reporting (release v0.1.3)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: eb03839cc36048f5 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=eb03839cc36048f5 + name: 'COVID-19: variation analysis reporting (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a70583aa531b7115 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a70583aa531b7115 + name: Parallel Accession Down (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 7b78e5630415f527 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7b78e5630415f527 + name: Parallel Accession Down (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 2dce5e80bae66d27 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2dce5e80bae66d27 + name: Parallel Accession Down (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: f54b4d76f7f9a589 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=f54b4d76f7f9a589 + name: 'COVID-19: variation analysis on WGS SE (release v0.1.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 03d1d2e0dc6e2024 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=03d1d2e0dc6e2024 + name: 'COVID-19: variation analysis on WGS SE (release v0.1.3)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c2af7a5dbfb5b023 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c2af7a5dbfb5b023 + name: 'COVID-19: variation analysis on WGS PE (release v0.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 07b74e4cf53cb633 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=07b74e4cf53cb633 + name: 'COVID-19: variation analysis on WGS PE (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 81122d30c64a52a6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=81122d30c64a52a6 + name: 'COVID-19: variation analysis on WGS PE (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7b7ef222ac4f9887 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7b7ef222ac4f9887 + name: 'COVID-19: variation analysis on WGS PE (release v0.2.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6dbac47941a804da + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6dbac47941a804da + name: 'COVID-19: variation analysis on ARTIC PE (release v0.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2573209308aaad23 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2573209308aaad23 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: fc216dfb0ec9ed41 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=fc216dfb0ec9ed41 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.3)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0be293debca8fb9b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ed20bd120064bab0 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ed20bd120064bab0 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a6f4371ef9bc1aab + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=a6f4371ef9bc1aab + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ee6dc47660540ba6 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=ee6dc47660540ba6 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.5)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - Pairwise sequence alignment + - SNP detection + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: b97532c398b821a2 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b97532c398b821a2 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - lofreq_filter + - tp_find_and_replace + - minimap2 + - samtools_view + - snpeff_sars_cov_2 + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - SNP detection + - Pairwise sequence alignment + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 7bdd9ad918edab0b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7bdd9ad918edab0b + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - snpeff_sars_cov_2 + - lofreq_filter + - minimap2 + - samtools_view + - tp_find_and_replace + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - SNP detection + - Pairwise sequence alignment + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 0f6a7bd5362e4a2b + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - snpeff_sars_cov_2 + - lofreq_filter + - minimap2 + - samtools_view + - tp_find_and_replace + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 2d9d4445a1871230 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.3)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 4d97068a725c975c + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=4d97068a725c975c + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.3.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: c832ecfa83bcda14 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14 + name: 'COVID-19: consensus construction (release v0.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: b8fc492025ad6ff0 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0 + name: 'COVID-19: consensus construction (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 522500fac247be6f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=522500fac247be6f + name: 'COVID-19: consensus construction (release v0.2.2)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 6c91fe92ef069d64 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64 + name: 'COVID-19: consensus construction (release v0.3)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2021-05-28' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Data handling + - Sequencing quality control + edam_topic: [] + id: 872f5bc9fdbbc619 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=872f5bc9fdbbc619 + name: Coffee QC + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - fasterq_dump + update_time: '2022-03-11' + versions: 2 +- create_time: '2021-03-15' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Data handling + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 48071c1720b2fd8d + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=48071c1720b2fd8d + name: AS Tomate + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - multiqc + - rna_star + - fasterq_dump + update_time: '2022-03-11' + versions: 2 +- create_time: '2022-01-26' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Variant calling + - Phylogenetic tree generation + edam_topic: [] + id: 65249196143d7930 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=65249196143d7930 + name: From Fastqs to VCFs and BAMs + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - __MERGE_COLLECTION__ + - trimmomatic + - snippy + - tb_variant_filter + update_time: '2022-03-10' + versions: 2 +- create_time: '2021-01-02' + creators: [] + doi: '' + edam_operation: + - Image analysis + edam_topic: [] + id: 1eaff95bfeb13890 + latest_version: 19 + license: null + link: https://usegalaxy.eu/published/workflow?id=1eaff95bfeb13890 + name: Registration of images based on landmarks + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ip_landmark_registration + - ip_projective_transformation + update_time: '2022-03-07' + versions: 19 +- create_time: '2022-02-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Genome assembly + - Sequence composition calculation + - Primer removal + - Aggregation + - Coding region prediction + - Scaffolding + - Genome annotation + - Visualisation + - Sequence trimming + - Transcriptome assembly + - Gene prediction + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 165089132248a0b0 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=165089132248a0b0 + name: TP OMICS DELAFONT + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - quast + - unicycler + - fasterq_dump + - prokka + - cutadapt + - busco + update_time: '2022-02-28' + versions: 4 +- create_time: '2022-02-25' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Annotation + edam_topic: [] + id: ca286c2fdc71e960 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960 + name: 'Workflow constructed from history ''''DEG: Normalization (DESeq2)''''' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - table_compute + - annotatemyids + - venn_list + - Cut1 + - tp_sort_header_tool + - tp_cat + - join1 + - ggplot2_heatmap2 + - tp_replace_in_column + - cat1 + - Filter1 + - comp1 + - deseq2 + - bg_uniq + update_time: '2022-02-28' + versions: 0 +- create_time: '2022-02-28' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 579dd1e95e76402f + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=579dd1e95e76402f + name: 'COVID-19: variation analysis on ARTIC PE data -iwc version 0.5' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + - iwc + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2022-02-28' + versions: 1 +- create_time: '2022-02-11' + creators: [] + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: e132370adf8f2838 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=e132370adf8f2838 + name: NPDN 2022 DADA2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - dada2_makeSequenceTable + - dada2_seqCounts + - dada2_learnErrors + - dada2_filterAndTrim + - dada2_mergePairs + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2022-02-24' + versions: 5 +- create_time: '2022-02-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 69eed719f9b5b99d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=69eed719f9b5b99d + name: 'Workflow: Overlapping features on opposite strands' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_cat + - gops_intersect_1 + - Filter1 + update_time: '2022-02-24' + versions: 1 +- create_time: '2022-02-18' + creators: [] + doi: '' + edam_operation: + - Image analysis + edam_topic: [] + id: e25f3ca3a1b4e4d8 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8 + name: Spot tracking + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ip_points_association_nn + - ip_spot_detection_2d + update_time: '2022-02-23' + versions: 4 +- create_time: '2022-02-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a372f693471beb56 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=a372f693471beb56 + name: Microbial Peptides PepQuery Validation Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Grouping1 + - pepquery + - Cut1 + - Filter1 + update_time: '2022-02-22' + versions: 2 +- create_time: '2022-02-21' + creators: [] + doi: '' + edam_operation: + - 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fastqc + - cshl_fastq_quality_filter + - fastqe + update_time: '2022-02-21' + versions: 0 +- create_time: '2022-02-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6d3ec4203b503810 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810 + name: fastqtofasta + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastq_stats + - cshl_fastx_reverse_complement + - fastq_to_fasta_python + update_time: '2022-02-11' + versions: 1 +- create_time: '2022-01-22' + creators: + - "Aur\xE9lien F. A. Moumbock" + - "Albert-Ludwigs-Universit\xE4t Freiburg" + doi: '' + edam_operation: [] + edam_topic: [] + id: 53cdd6bf98e4c77d + latest_version: 52 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=53cdd6bf98e4c77d + name: Zauberkugel + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + - computational-chemistry + tools: + - sort1 + - split_file_to_collection + - tp_cat + - rdconf + - openbabel_addh + - ctb_alignit + update_time: '2022-02-07' + versions: 52 +- create_time: '2022-02-07' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d5780c37232e3181 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=d5780c37232e3181 + name: Workflow constructed 'Test FASTQ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + - fastqe + update_time: '2022-02-07' + versions: 0 +- create_time: '2022-02-02' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 06544e74f583fd05 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=06544e74f583fd05 + name: 'COVID-19: consensus construction - iwc version 0.3' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-02-07' + versions: 1 +- create_time: '2022-02-05' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 498311923691884b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=498311923691884b + name: SNP-Cromosoma 22 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - 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tp_cat + - tp_replace_in_line + - tp_sed_tool + - tp_grep_tool + - samtools_view + - __MERGE_COLLECTION__ + - tb_profiler_profile + update_time: '2022-02-04' + versions: 10 +- create_time: '2022-02-04' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 927d24dcde139b9c + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=927d24dcde139b9c + name: Workflow constructed from history 'Test RNA-Seq 1' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - multiqc + - featurecounts + - hisat2 + update_time: '2022-02-04' + versions: 0 +- create_time: '2022-02-04' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 91d4aabba7ad40c8 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=91d4aabba7ad40c8 + name: Workflow constructed from history 'Clase 2' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - multiqc + update_time: '2022-02-04' + versions: 0 +- create_time: '2022-02-04' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + edam_topic: [] + id: 7036a6cf67d53bc7 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=7036a6cf67d53bc7 + name: Workflow constructed from history 'RNA-Seq 2 Matriz de Conteo' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - limma_voom + update_time: '2022-02-04' + versions: 0 +- create_time: '2022-02-04' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + edam_topic: [] + id: ad3be77eb2e8c10e + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=ad3be77eb2e8c10e + name: Workflow constructed from history 'HISTORIA 3' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - limma_voom + update_time: '2022-02-04' + versions: 0 +- create_time: '2022-02-04' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + edam_topic: [] + id: 8f095e5b9594b098 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=8f095e5b9594b098 + name: Workflow constructed from history 'RNA-seq tutorial 2' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - limma_voom + update_time: '2022-02-04' + versions: 0 +- create_time: '2022-01-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2ebf65efe8ca4a7f + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f + name: From VCFs to SNP distance matrix (OLD) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cshl_fasta_formatter + - addName + - tp_cat + - tp_awk_tool + - tb_variant_filter + - snp_dists + - snp_sites + - bcftools_consensus + - melt + update_time: '2022-02-04' + versions: 11 +- create_time: '2022-01-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - 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hyphy_fade + - hyphy_slac + - hyphy_summary + - hyphy_fel + - hyphy_cfel + - hyphy_busted + - hyphy_meme + - hyphy_annotate + - hyphy_bgm + - hyphy_prime + update_time: '2022-01-26' + versions: 1 +- create_time: '2021-11-22' + creators: [] + doi: '' + edam_operation: + - Mapping + - Sequence motif discovery + edam_topic: [] + id: d3a4e6cc1b4565e5 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=d3a4e6cc1b4565e5 + name: Motif Analysis of Two Sets of Peaks with Homer (Enriching one on the other) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ATAC + - chiara + tools: + - bedtools_intersectbed + - __UNZIP_COLLECTION__ + - homer_findMotifsGenome + update_time: '2022-01-26' + versions: 3 +- create_time: '2021-06-23' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 9ac15b644c805a2b + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b + name: June 22 Test Encyclopedia raw + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - encyclopedia_quantify + - encyclopedia_searchtolib + - msconvert + update_time: '2022-01-24' + versions: 1 +- create_time: '2021-05-04' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 14f9c2099db30570 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=14f9c2099db30570 + name: 05042021_EncyclopeDIA Standard Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - encyclopedia_quantify + - encyclopedia_searchtolib + - msconvert + update_time: '2022-01-24' + versions: 3 +- create_time: '2022-01-23' + creators: [] + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + edam_topic: [] + id: 3480204a99bf4a35 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3480204a99bf4a35 + name: VGP optimization purge_dups partial + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - merqury + - purge_dups + update_time: '2022-01-23' + versions: 0 +- create_time: '2022-01-23' + creators: [] + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Visualisation + - Sequence assembly validation + edam_topic: [] + id: 69be0fb8276753ec + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=69be0fb8276753ec + name: VGP optimization purge_dups complete + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + - quast + - merqury + - purge_dups + update_time: '2022-01-23' + versions: 2 +- create_time: '2022-01-21' + creators: + - FredBGA + doi: '' + edam_operation: [] + edam_topic: [] + id: 1c85626b12cf3ac5 + latest_version: 5 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1c85626b12cf3ac5 + name: Sed - optional NO - input param + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Dev + tools: + - tp_sed_tool + update_time: '2022-01-21' + versions: 5 +- create_time: '2021-12-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 428be4c7d1fd828f + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=428be4c7d1fd828f + name: Community abundance and taxonomic/phylogenetic diversity EBV workflow - Count + data + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - pampa_glmcomm + - pampa_plotglm + - pampa_communitymetrics + update_time: '2022-01-13' + versions: 2 +- create_time: '2019-10-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b0b6c8756070650b + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b + name: Complete EBV workflow example from GBIF data with RStudio and Wallace + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:EBVuseable + - name:EBVready + - name:EBVderivedmodelled + tools: + - Count1 + - spocc_occ + - interactive_tool_wallace + - interactive_tool_rstudio + - Summary_Statistics1 + - gdal_ogr2ogr + - Filter1 + update_time: '2022-01-13' + versions: 9 +- create_time: '2022-01-11' + creators: [] + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: 48d0dc424e71d8c2 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=48d0dc424e71d8c2 + name: dada2 main pipeline (16S/18S) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - dada2_makeSequenceTable + - __UNZIP_COLLECTION__ + - tp_cat + - dada2_seqCounts + - dada2_assignTaxonomyAddspecies + - tp_tail_tool + - tp_replace_in_column + - dada2_learnErrors + - dada2_filterAndTrim + - tp_head_tool + - dada2_mergePairs + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2022-01-11' + versions: 6 +- create_time: '2021-11-16' + creators: + - Koen Wijnans + doi: '' + edam_operation: + - Formatting + - Variant calling + - Sequence contamination filtering + - Pairwise sequence alignment + - Scatter plot plotting + - Box-Whisker plot plotting + - Sequence assembly visualisation + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fc0b9efa7d2e61e6 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6 + name: Coverage + Consensus HA+NA + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - __EXTRACT_DATASET__ + - collapse_dataset + - samtools_stats + - porechop + - samtools_depth + - Convert characters1 + - sort1 + - table_compute + - nanoplot + - seq_filter_by_id + - ngsutils_bam_filter + - minimap2 + - comp1 + - Show beginning1 + - Filter1 + - Cut1 + - bandage_info + - ncbi_acc_download + - tp_easyjoin_tool + - bioext_bam2msa + - ivar_consensus + - ncbi_blastn_wrapper + update_time: '2022-01-03' + versions: 3 +- create_time: '2021-12-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 46b4ad3ce0b7bc0b + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=46b4ad3ce0b7bc0b + name: '''GTN - CESM F2000 f19_f19_mg17 tutorial''' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cesm + update_time: '2021-12-29' + versions: 2 +- create_time: '2021-12-28' + creators: + - Anne Fouilloux + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 0c6dd9e75d9a2130 + latest_version: 83 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130 + name: GTN 'Pangeo 101 for everyone - Xarray' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - pangeo + - climate + - copernicus + - GTN + tools: + - xarray_metadata_info + - __EXTRACT_DATASET__ + - xarray_mapplot + - xarray_netcdf2netcdf + - graphicsmagick_image_montage + - regexColumn1 + - xarray_coords_info + - ggplot2_point + - xarray_select + - __MERGE_COLLECTION__ + - climate_stripes + update_time: '2021-12-28' + versions: 83 +- create_time: '2021-12-22' + creators: + - Anne Fouilloux + doi: '' + edam_operation: [] + edam_topic: [] + id: b2a26b300b596ff3 + latest_version: 10 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=b2a26b300b596ff3 + name: Pangeo Jupyter Notebook + number_of_steps: null + source: https://usegalaxy.eu + tags: + - pangeo + - climate + - big-data + - geosciences + tools: + - interactive_tool_pangeo_notebook + update_time: '2021-12-23' + versions: 10 +- create_time: '2020-12-03' + creators: [] + doi: '' + edam_operation: + - Formatting + - Statistical calculation + - Genome indexing + - Read mapping + - Variant calling + - Sequence contamination filtering + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 45fc2dada84d251e + latest_version: 15 + license: null + link: https://usegalaxy.eu/published/workflow?id=45fc2dada84d251e + name: VA-direct SARS-CoV-2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - ngsutils_bam_filter + - ivar_variants + - qualimap_bamqc + - ivar_consensus + - bamleftalign + - bwa_mem + update_time: '2021-12-21' + versions: 15 +- create_time: '2021-12-09' + creators: [] + doi: '' + edam_operation: + - Genome annotation + - Sequence visualisation + edam_topic: [] + id: 0de5fcc38ef1501d + latest_version: 26 + license: null + link: https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d + name: Mitogenome MITOS2 annotation and CIRCOS plot + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - circos_interval_to_tile + - Cut1 + - Add_a_column1 + - tp_cat + - circos_interval_to_text + - tp_grep_tool + - tp_replace_in_column + - tp_awk_tool + - mitos2 + - param_value_from_file + - circos + - fasta_compute_length + update_time: '2021-12-20' + versions: 26 +- create_time: '2021-12-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 58cc9091bb0bd18f + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=58cc9091bb0bd18f + name: CMB_final_assignment_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snpEff + - snpSift_vcfCheck + - snpSift_filter + - snpSift_rmInfo + update_time: '2021-12-14' + versions: 5 +- create_time: '2021-12-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ecd1cf44f3bd2ed5 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=ecd1cf44f3bd2ed5 + name: 'Filter variants with highest impact from PGP Canada: Participant 16. JCMD + 3' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snpEff + - snpSift_filter + - snpSift_rmInfo + update_time: '2021-12-12' + versions: 2 +- create_time: '2021-12-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a08279c2a305afff + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=a08279c2a305afff + name: Workflow on read mapping with BWA + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - tp_sort_header_tool + - trim_galore + - bamFilter + - bwa + - samtools_flagstat + - deeptools_bam_coverage + update_time: '2021-12-10' + versions: 0 +- create_time: '2021-12-09' + creators: + - JC Marchiori Dias + doi: '' + edam_operation: [] + edam_topic: [] + id: 7a9f2b7263f2ea57 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=7a9f2b7263f2ea57 + name: 'Filter variants with highest impact from PGP Canada: Participant 16. JCMD + 2' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snpEff + - snpSift_filter + - snpSift_rmInfo + update_time: '2021-12-09' + versions: 4 +- create_time: '2021-12-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Genome assembly + - De-novo assembly + - Sequence composition calculation + - Pairwise sequence alignment + - Visualisation + - Cross-assembly + - Mapping assembly + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 8b2f53745e720d0f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f + name: Metagenome of water samples + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fasta_filter_by_length + - quast + - flye + - racon + - krona-text + - kraken2 + - porechop + - minimap2 + - bandage_image + update_time: '2021-12-03' + versions: 1 +- create_time: '2020-11-22' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + - Antimicrobial resistance prediction + - Genome assembly + - Multilocus sequence typing + edam_topic: [] + id: 49c46d7653d6c349 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349 + name: AMG2021 - simple workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - abricate + - spades + - mlst + - fasta-stats + - kraken2 + update_time: '2021-12-02' + versions: 4 +- create_time: '2021-11-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: c7e1aee909c9b483 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=c7e1aee909c9b483 + name: Workflow constructed from history 'DAY 2 - Work Done' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastq_groomer + - bowtie2 + - htseq_count + update_time: '2021-11-22' + versions: 1 +- create_time: '2021-11-16' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: eb3cfa4d1f05fc0e + latest_version: 24 + license: null + link: https://usegalaxy.eu/published/workflow?id=eb3cfa4d1f05fc0e + name: TopHat with Groomer_Workflow_Final Version + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - tophat2 + - htseq_count + - multiqc + - fastq_groomer + update_time: '2021-11-21' + versions: 24 +- create_time: '2021-11-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: cf9dc7ad34c81fa2 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=cf9dc7ad34c81fa2 + name: 'workflow from scratch ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastq_groomer + - bowtie2 + - htseq_count + update_time: '2021-11-17' + versions: 8 +- create_time: '2021-11-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 70b1c40b818cc320 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=70b1c40b818cc320 + name: Workflow constructed from history 'Analsysi of FastQ file' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fastq_groomer + - bowtie2 + - htseq_count + update_time: '2021-11-16' + versions: 4 +- create_time: '2021-02-05' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: a4d6b9dc6b396933 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933 + name: Metaproteomics_GTN + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2021-11-14' + versions: 4 +- create_time: '2021-11-09' + creators: [] + doi: '' + edam_operation: + - Query and retrieval + - Statistical inference + - Quantification + - Filtering + - Indexing + - Heat map generation + - Functional clustering + - Visualisation + - Differential protein expression analysis + - Principal component visualisation + edam_topic: [] + id: ce7f7c6eef526d67 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67 + name: metaquantome-taxonomy-workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - proteomics + tools: + - metaquantome_stat + - metaquantome_viz + - metaquantome_sample + - metaquantome_expand + - metaquantome_filter + - metaquantome_db + update_time: '2021-11-09' + versions: 2 +- create_time: '2021-04-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome alignment + - Sequence composition calculation + - Genome indexing + - Read mapping + - Variant calling + - Validation + - Copy number estimation + - Generation + - Sequencing quality control + - Sequence alignment + - Sequence visualisation + edam_topic: [] + id: 220961d803697f54 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=220961d803697f54 + name: MIRACUM - somatic variant discovery from WES data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MIRACUM + tools: + - fastqc + - tp_text_file_with_recurring_lines + - trimmomatic + - __EXTRACT_DATASET__ + - split_file_to_collection + - collapse_dataset + - __RELABEL_FROM_FILE__ + - tp_replace_in_column + - tp_find_and_replace + - control_freec + - datamash_ops + - varscan_somatic + - Grep1 + - Convert characters1 + - gemini_annotate + - compose_text_param + - samtools_calmd + - multiqc + - __MERGE_COLLECTION__ + - Add_a_column1 + - tp_replace_in_line + - samtools_rmdup + - __SORTLIST__ + - qualimap_bamqc + - gemini_query + - __APPLY_RULES__ + - __FILTER_FROM_FILE__ + - snpEff + - param_value_from_file + - __BUILD_LIST__ + - datamash_transpose + - circos + - bwa_mem + - Filter1 + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - gemini_load + - tp_easyjoin_tool + - bamleftalign + - samtools_view + update_time: '2021-11-09' + versions: 2 +- create_time: '2021-05-25' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Taxonomic classification + - Species frequency estimation + edam_topic: [] + id: 5ce8a472e6e95c60 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60 + name: 'Metatranscriptomics-WF3: Functional Information (quick)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + tools: + - humann_split_stratified_table + - combine_metaphlan2_humann2 + - Grep1 + - humann_renorm_table + - humann_unpack_pathways + - humann_rename_table + - humann_regroup_table + update_time: '2021-11-09' + versions: 8 +- create_time: '2021-05-25' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Taxonomic classification + - Species frequency estimation + edam_topic: [] + id: 23dd2253da51e22e + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e + name: 'Metatranscriptomics-WF3: Functional Information' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + tools: + - humann_split_stratified_table + - combine_metaphlan2_humann2 + - Grep1 + - humann_renorm_table + - humann + - humann_unpack_pathways + - humann_rename_table + - humann_regroup_table + update_time: '2021-11-09' + versions: 6 +- create_time: '2021-11-09' + creators: [] + doi: '' + edam_operation: + - Query and retrieval + - Statistical inference + - Quantification + - Filtering + - Indexing + - Heat map generation + - Functional clustering + - Visualisation + - Differential protein expression analysis + - Principal component visualisation + edam_topic: [] + id: dc438d4ae1866df8 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8 + name: metaquantome-function-worklow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - proteomics + tools: + - metaquantome_stat + - metaquantome_viz + - metaquantome_sample + - metaquantome_expand + - metaquantome_filter + - metaquantome_db + update_time: '2021-11-09' + versions: 4 +- create_time: '2021-11-09' + creators: [] + doi: '' + edam_operation: + - Formatting + - Visualisation + - Prediction and recognition + - Filtering + - Label-free quantification + edam_topic: [] + id: d0e062aee910086a + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=d0e062aee910086a + name: metaQuantome_datacreation_workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - tp_replace_in_line + - query_tabular + - tp_replace_in_column + - flashlfq + - peptide_shaker + - search_gui + - unipept + - msconvert + - regex1 + - Filter1 + update_time: '2021-11-09' + versions: 5 +- create_time: '2021-10-30' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Sequence contamination filtering + - Statistical calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 606a04c4aa95d010 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=606a04c4aa95d010 + name: Tetrahymena Variant Calling and Annotation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - mimodd_covstats + - mimodd_varextract + - mimodd_rebase + - mimodd_varcall + - samtools_rmdup + - bcftools_norm + - snpEff + - bamleftalign + - samtools_view + - bowtie2 + update_time: '2021-10-30' + versions: 4 +- create_time: '2021-10-29' + creators: + - Graham Etherington + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + edam_topic: [] + id: 9a52516ec0b539ea + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=9a52516ec0b539ea + name: Single Cell reads to expression matrix + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rna_star + - collection_column_join + - featurecounts + - tp_sed_tool + update_time: '2021-10-29' + versions: 8 +- create_time: '2021-10-14' + creators: + - Erwan Corre + - "St\xE9phanie Robin" + - Anthony Bretaudeau + - Alexandre Cormier + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Scaffolding + - Visualisation + - Transcriptome assembly + - Cross-assembly + - Mapping assembly + - Sequence assembly validation + edam_topic: [] + id: 30b514cfb9cce524 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524 + name: Genome Assembly + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fasta-stats + - quast + - busco + - flye + update_time: '2021-10-26' + versions: 8 +- create_time: '2021-09-09' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 7705b1e25110baf4 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=7705b1e25110baf4 + name: Iris Analysis Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2021-10-21' + versions: 1 +- create_time: '2021-10-05' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Formatting + - Data handling + - Read pre-processing + - Read mapping + - Primer removal + edam_topic: [] + id: 41b5f0d519404df7 + latest_version: 18 + license: null + link: https://usegalaxy.eu/published/workflow?id=41b5f0d519404df7 + name: Workflow get bw from rossi et al + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - __EXTRACT_DATASET__ + - deeptools_bam_coverage + - trim_galore + - fasterq_dump + - __FLATTEN__ + - picard_MarkDuplicates + - bowtie2 + update_time: '2021-10-19' + versions: 18 +- create_time: '2021-10-18' + creators: + - null + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Taxonomic classification + - Genome indexing + - Sequence composition calculation + - Read mapping + - Visualisation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ee0005a5487653ba + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=ee0005a5487653ba + name: Metatranscriptomics - analyze human RNA-seq data with Kraken (imported from + uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metatranscriptomics + - Kraken + - RNA-seq + - microbiome + tools: + - fastqc + - Kraken2Tax + - trimmomatic + - taxonomy_krona_chart + - bwa + - kraken2 + - picard_SamToFastq + - samtools_view + update_time: '2021-10-18' + versions: 2 +- create_time: '2021-09-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6a48604ef9ceb8b8 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6a48604ef9ceb8b8 + name: 'Overlapping genes workflow ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cat1 + - gops_intersect_1 + - Filter1 + update_time: '2021-09-28' + versions: 1 +- create_time: '2021-09-24' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 57769c948e14f9ac + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=57769c948e14f9ac + name: 'COVID-19: variation analysis on WGS SE data - iwc version 0.1.2' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2021-09-24' + versions: 1 +- create_time: '2021-09-24' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 1761092d0e7deece + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=1761092d0e7deece + name: 'COVID-19: variation analysis on WGS PE data - iwc version 0.2.1' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2021-09-24' + versions: 1 +- create_time: '2021-09-24' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0189bab68f828d86 + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=0189bab68f828d86 + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar based - iwc version 0.1 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2021-09-24' + versions: 1 +- create_time: '2021-09-24' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 476db04368d5e90c + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=476db04368d5e90c + name: 'COVID-19: variation analysis of ARTIC ONT data - iwc version 0.3' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + - iwc + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2021-09-24' + versions: 1 +- create_time: '2021-09-01' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Sequence assembly validation + edam_topic: [] + id: 45c0933b5c522628 + latest_version: 0 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=45c0933b5c522628 + name: VGP Bionano (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cat1 + - param_value_from_file + - bionano_scaffold + - quast + update_time: '2021-09-01' + versions: 0 +- create_time: '2021-01-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fdd60d4121673f62 + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=fdd60d4121673f62 + name: EncyclopeDIA_peptide_to_MetaQuantome + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - tp_awk_tool + - query_tabular + update_time: '2021-08-31' + versions: 7 +- create_time: '2021-08-30' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Sequence trimming + - Visualisation + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: d67299c34e63f3d9 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=d67299c34e63f3d9 + name: hifi_workflow.ga + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - hifiasm + - quast + - genomescope + - Add_a_column1 + - merqury + - tp_grep_tool + - tp_cut_tool + - cat1 + - cutadapt + - gfa_to_fa + - Convert characters1 + - tp_find_and_replace + - minimap2 + - meryl + - param_value_from_file + - busco + - purge_dups + update_time: '2021-08-30' + versions: 1 +- create_time: '2021-08-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 60a45de522b8b695 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=60a45de522b8b695 + name: paired + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - trim_galore + - featurecounts + - hisat2 + update_time: '2021-08-30' + versions: 6 +- create_time: '2021-08-21' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Aggregation + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Mapping assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: c48807045e258dd8 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c48807045e258dd8 + name: Workflow constructed from history 'ojonugwa sub team Metagenomics A' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - HackBioInternship2021 + tools: + - nanoplot + - staramr_search + - PlasFlow + - racon + - unicycler + - miniasm + - gfa_to_fa + - minimap2 + - bandage_image + update_time: '2021-08-21' + versions: 0 +- create_time: '2021-08-21' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Aggregation + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Mapping assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: 39837ca09374598b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=39837ca09374598b + name: Workflow constructed from history 'Premnath sub team Metagenomics A' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - HackBioInternship2021 + tools: + - nanoplot + - staramr_search + - PlasFlow + - racon + - unicycler + - miniasm + - gfa_to_fa + - minimap2 + - bandage_image + update_time: '2021-08-21' + versions: 0 +- create_time: '2021-08-21' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Aggregation + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Mapping assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: 249c115413f17f28 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=249c115413f17f28 + name: Workflow constructed from history 'Isha sub group Team Metagenomics A' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - HackBioInternship2021 + tools: + - nanoplot + - staramr_search + - PlasFlow + - racon + - unicycler + - miniasm + - gfa_to_fa + - minimap2 + - bandage_image + update_time: '2021-08-21' + versions: 0 +- create_time: '2021-08-20' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Aggregation + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Mapping assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: dc7107896a3f2964 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964 + name: Workflow constructed from history 'Rishikesh sub team' Team Metagenomics A + number_of_steps: null + source: https://usegalaxy.eu + tags: + - HackBio2021Internship + tools: + - nanoplot + - staramr_search + - PlasFlow + - racon + - unicycler + - miniasm + - gfa_to_fa + - minimap2 + - bandage_image + update_time: '2021-08-20' + versions: 1 +- create_time: '2021-08-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c1bbcf17d150d95a + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c1bbcf17d150d95a + name: Workflow constructed from history 'Metagenomics' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: [] + update_time: '2021-08-20' + versions: 0 +- create_time: '2021-08-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: bbe2a1615c8faaae + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=bbe2a1615c8faaae + name: single + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - trim_galore + - featurecounts + - hisat2 + update_time: '2021-08-12' + versions: 1 +- create_time: '2021-08-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 443ea80b36d862f5 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=443ea80b36d862f5 + name: small + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - trim_galore + - bowtie2 + - featurecounts + update_time: '2021-08-12' + versions: 2 +- create_time: '2021-08-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: eb8168bc01249596 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=eb8168bc01249596 + name: Total-rna-seq-workflow-DE + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - collection_column_join + - trim_galore + - featurecounts + - hisat2 + update_time: '2021-08-11' + versions: 0 +- create_time: '2021-08-09' + creators: + - "Melanie F\xF6ll" + doi: '' + edam_operation: [] + edam_topic: [] + id: e573c6b697524e3a + latest_version: 1 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=e573c6b697524e3a + name: 'Bladder MSI WF6: annotating potential identities' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - bladder_MSI + - MS_imaging + - shared + tools: + - cat1 + - datamash_ops + - Remove beginning1 + - join_files_on_column_fuzzy + update_time: '2021-08-09' + versions: 1 +- create_time: '2021-06-22' + creators: + - "Melanie F\xF6ll" + doi: '' + edam_operation: [] + edam_topic: [] + id: fb233e418d015649 + latest_version: 9 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=fb233e418d015649 + name: 'Bladder MSI WF5: visualization' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - bladder_MSI + - MS_imaging + - shared + tools: + - cardinal_filtering + - cardinal_mz_images + - cardinal_preprocessing + - cardinal_spectra_plots + - Show beginning1 + - Filter1 + update_time: '2021-08-09' + versions: 9 +- create_time: '2021-08-02' + creators: + - "Melanie F\xF6ll" + doi: '' + edam_operation: [] + edam_topic: [] + id: 9e497c5c9e64d9b3 + latest_version: 6 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3 + name: 'Bladder MSI WF4: classification infiltrating vs. non-infiltrating' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - bladder_MSI + - MS_imaging + - shared + tools: + - cardinal_filtering + - Remove beginning1 + - addName + - cardinal_classification + - datamash_ops + - tp_easyjoin_tool + - cat1 + - param_value_from_file + - sklearn_train_test_split + - Filter1 + update_time: '2021-08-09' + versions: 6 +- create_time: '2021-07-27' + creators: + - "Melanie F\xF6ll" + doi: '' + edam_operation: [] + edam_topic: [] + id: f4a55ef0d4c2cd97 + latest_version: 8 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97 + name: 'Bladder MSI WF3: classification tumor vs. stroma' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - bladder_MSI + - MS_imaging + - shared + tools: + - Remove beginning1 + - addName + - cardinal_filtering + - Cut1 + - cardinal_classification + - datamash_ops + - tp_easyjoin_tool + - cat1 + - tp_sorted_uniq + - param_value_from_file + - sklearn_train_test_split + - Filter1 + update_time: '2021-08-09' + versions: 8 +- create_time: '2021-07-22' + creators: + - "Melanie F\xF6ll" + doi: '' + edam_operation: [] + edam_topic: [] + id: 7ee6976f69131683 + latest_version: 9 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=7ee6976f69131683 + name: 'Bladder MSI WF2: data handling and preprocessing' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - bladder_MSI + - MS_imaging + - shared + tools: + - cardinal_combine + - cardinal_filtering + - cardinal_preprocessing + - cardinal_quality_report + - cardinal_data_exporter + - maldi_quant_peak_detection + - __BUILD_LIST__ + - Filter1 + update_time: '2021-08-09' + versions: 9 +- create_time: '2021-07-22' + creators: + - "Melanie F\xF6ll" + doi: '' + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: 03e8b0d3dcedc092 + latest_version: 12 + license: MIT + link: https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092 + name: 'Bladder MSI WF1: Co-registration and ROI extraction' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - bladder_MSI + - MS_imaging + - shared + tools: + - Remove beginning1 + - cardinal_mz_images + - imagecoordinates_flipaxis + - addName + - tp_cat + - tp_replace_in_line + - datamash_ops + - Cut1 + - tp_easyjoin_tool + - ip_landmark_registration + - cat1 + - graphicsmagick_image_convert + - ip_coordinates_of_roi + - ip_projective_transformation_points + - ip_scale_image + - ip_viz_overlay_moving_and_fixed_image + update_time: '2021-08-09' + versions: 12 +- create_time: '2021-08-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 924edc19e0653870 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=924edc19e0653870 + name: GTN_ENA_upload_workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ena_upload + update_time: '2021-08-06' + versions: 1 +- create_time: '2021-04-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Validation + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ff2fd4a4bb27d859 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=ff2fd4a4bb27d859 + name: MIRACUM - variant discovery from gene panel data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MIRACUM + tools: + - fastqc + - trimmomatic + - snpSift_extractFields + - __EXTRACT_DATASET__ + - split_file_to_collection + - collapse_dataset + - tp_replace_in_column + - tp_find_and_replace + - lofreq_alnqual + - datamash_ops + - lofreq_filter + - Grep1 + - gemini_annotate + - samtools_calmd + - multiqc + - bedtools_mergebed + - tp_replace_in_line + - Add_a_column1 + - __SORTLIST__ + - gemini_query + - snpEff + - addValue + - datamash_transpose + - Filter1 + - bwa_mem + - Cut1 + - bg_column_arrange_by_header + - add_line_to_file + - bedtools_genomecoveragebed + - gemini_load + - lofreq_call + - lofreq_indelqual + - tp_easyjoin_tool + - bamleftalign + - samtools_view + update_time: '2021-07-29' + versions: 2 +- create_time: '2021-07-21' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: db10c092fad70d69 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=db10c092fad70d69 + name: 2021-July-21_workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - rnaspades + - multiqc + - bowtie2 + update_time: '2021-07-21' + versions: 1 +- create_time: '2021-06-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 86f3d5053996d3e8 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=86f3d5053996d3e8 + name: 'molecular docking ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - chembl + - openbabel_svg_depiction + - prepare_box + - tp_grep_tool + - prepare_receptor + - CONVERTER_SMILES_to_sdf + - docking + - openbabel_compound_convert + update_time: '2021-07-05' + versions: 0 +- create_time: '2021-06-22' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 87c21b682af78ec9 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9 + name: June 22 GTN EncyclopeDIA workflow raw inputs + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:EncyclopeDIA + - name:GTN + tools: + - encyclopedia_quantify + - encyclopedia_searchtolib + - msconvert + update_time: '2021-06-24' + versions: 3 +- create_time: '2021-06-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Phylogenetic analysis + - Formatting + - Sequence alignment analysis + - Phylogenetic inference + - Primer removal + - Species frequency estimation + - Sequence similarity search + - Sequencing quality control + - Taxonomic classification + - Sequence composition calculation + - Sequence comparison + - Phylogenetic tree visualisation + - Validation + - Sequence trimming + - Visualisation + - Phylogenetic tree analysis + - Conversion + - Read pre-processing + - Nucleic acid sequence analysis + - Phylogenetic tree editing + edam_topic: [] + id: a8f829deb69b30ab + latest_version: 14 + license: null + link: https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab + name: Taxonomic and functional community profiling of raw metagenomic shotgun data + workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - asaim + tools: + - fastqc + - group_humann2_uniref_abundances_to_go + - graphlan_annotate + - humann_regroup_table + - metaphlan + - taxonomy_krona_chart + - cutadapt + - Grep1 + - multiqc + - graphlan + - humann_unpack_pathways + - export2graphlan + - fastq_paired_end_interlacer + - humann2_genefamilies_genus_level + - humann + - combine_metaphlan2_humann2 + - format_metaphlan2_output + - Cut1 + - humann_renorm_table + - bg_sortmerna + - humann_rename_table + update_time: '2021-06-24' + versions: 14 +- create_time: '2021-06-12' + creators: + - "Jos\xE9 Mar\xEDa Ponce Bernab\xE9" + - "David Ruiz Guillam\xF3n" + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Gene-set enrichment analysis + - Primer removal + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7136ce9f18c74853 + latest_version: 10 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853 + name: Differential Expression RNA-Seq + number_of_steps: null + source: https://usegalaxy.eu + tags: + - rna-seq + - rnaseq + - differential + - expression + - yeast + - deseq2 + - differential-expression + - enrichment + - goenrichment + - rna + - qualimap + - fastqc + - volcano + - volcanoplot + - trimgalore + - trim + - stringtie + - rnastar + - star + - mapping + - quality + tools: + - fastqc + - Remove beginning1 + - stringtie + - trim_galore + - qualimap_rnaseq + - join1 + - tp_cut_tool + - qualimap_bamqc + - volcanoplot + - goenrichment + - rna_star + - deseq2 + - Filter1 + update_time: '2021-06-21' + versions: 10 +- create_time: '2021-06-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Sequence analysis + - Generation + - Sequence alignment + - Genetic variation analysis + - Sequencing quality control + edam_topic: [] + id: b3b094f1bdbaa04a + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=b3b094f1bdbaa04a + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gemini_inheritance + - gemini_load + - bwa_mem + - samtools_rmdup + - bcftools_norm + - snpEff_download + - snpEff + - samtool_filter2 + - freebayes + update_time: '2021-06-19' + versions: 0 +- create_time: '2021-06-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Sequence analysis + - Generation + - Sequence alignment + - Genetic variation analysis + - Sequencing quality control + edam_topic: [] + id: b82a4065be048ef6 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=b82a4065be048ef6 + name: "gi\u1EA3i tr\xECnh t\u1EF1 exon" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - gemini_inheritance + - gemini_load + - bwa_mem + - samtools_rmdup + - bcftools_norm + - snpEff_download + - snpEff + - samtool_filter2 + - freebayes + update_time: '2021-06-19' + versions: 3 +- create_time: '2021-06-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fb425d6accf3ca55 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=fb425d6accf3ca55 + name: Single molecule energy minimization + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + - 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ggplot2_point + - tp_find_and_replace + - xarray_select + update_time: '2021-06-15' + versions: 5 +- create_time: '2021-05-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c39a79bb45b2566e + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c39a79bb45b2566e + name: MD protein-ligand workflow (from PDB structure) (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + - moleculardynamics + - computational-chemistry + tools: + - get_pdb + - ambertools_acpype + - gmx_sim + - gmx_editconf + - gmx_em + - gmx_setup + - tp_grep_tool + - gmx_solvate + - gmx_merge_topology_files + - openbabel_compound_convert + update_time: '2021-06-14' + versions: 0 +- create_time: '2021-06-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b610849d70c1e225 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=b610849d70c1e225 + name: Workflow for Climate tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: + - climate + tools: + - c3s + update_time: '2021-06-11' + versions: 2 +- create_time: '2021-06-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ac5b66c42681e7a8 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=ac5b66c42681e7a8 + name: Retrieve climate data from Copernicus + number_of_steps: null + source: https://usegalaxy.eu + tags: + - climate + tools: + - c3s + update_time: '2021-06-11' + versions: 2 +- create_time: '2021-05-21' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + edam_topic: [] + id: cfd37e9e307e5d3d + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=cfd37e9e307e5d3d + name: ONT -- Metagenomics-Kraken2-Krona + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ONT + tools: + - tp_replace_in_line + - kraken2 + - taxonomy_krona_chart + - datamash_reverse + update_time: '2021-06-10' + versions: 0 +- create_time: '2021-06-07' + creators: [] + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Global alignment + - Sequence analysis + - DNA mapping + - Sequence alignment + - Genetic variation analysis + edam_topic: [] + id: 04a4dcac3fd922c5 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5 + name: decontamination protocol + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - samtools_fastx + - ngmlr + - filter_by_fasta_ids + - fastq_to_fasta_python + - 'EMBOSS: trimest102' + - trimmer + update_time: '2021-06-09' + versions: 3 +- create_time: '2021-05-29' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: d9e7a940b2d410bc + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc + name: IIT Bombay Metaproteomics PXD025080 Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - unipept + - search_gui + - peptide_shaker + update_time: '2021-05-29' + versions: 4 +- create_time: '2021-05-25' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + - Phylogenetic inference + - Phylogenetic tree visualisation + - Visualisation + - Conversion + - Phylogenetic tree analysis + - Nucleic acid sequence analysis + - Phylogenetic tree editing + edam_topic: [] + id: 19de5cbae7f48103 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103 + name: 'Metatranscriptomcis-WF2: Community Profile' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + tools: + - taxonomy_krona_chart + - Cut1 + - export2graphlan + - graphlan + - graphlan_annotate + - metaphlan + update_time: '2021-05-25' + versions: 2 +- create_time: '2021-05-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence alignment analysis + - Sequence composition calculation + - Sequence comparison + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence similarity search + - Sequencing quality control + edam_topic: [] + id: f6e8a63283262518 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=f6e8a63283262518 + name: 'Metatranscriptomics-WF1: Preprocessing' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + tools: + - fastqc + - fastq_paired_end_interlacer + - cutadapt + - multiqc + - bg_sortmerna + update_time: '2021-05-25' + versions: 2 +- create_time: '2016-07-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d3a8741131485af2 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=d3a8741131485af2 + name: 1000_top_peaks_60bp_fasta_for_MEME' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Add_a_column1 + - Show beginning1 + - Cut1 + - Extract genomic DNA 1 + update_time: '2021-05-24' + versions: 6 +- create_time: '2021-05-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cdc8e12dea66774c + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=cdc8e12dea66774c + name: ARTIC PE variation analysis from nested samples + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - __ZIP_COLLECTION__ + - collapse_dataset + update_time: '2021-05-21' + versions: 3 +- create_time: '2021-05-18' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: e764c594f070f107 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=e764c594f070f107 + name: Workflow constructed from history 'analysis of gene expression' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - deg_annotate + - cat1 + - deseq2 + - Filter1 + update_time: '2021-05-18' + versions: 0 +- create_time: '2021-04-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 933ab5e7fe13a8e0 + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=933ab5e7fe13a8e0 + name: Spawn of Daughter of Blastn + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - table_compute + - tp_split_on_column + - collapse_dataset + - fasta2tab + - join1 + - tab2fasta + - trimmer + - ncbi_blastn_wrapper + - ncbi_makeblastdb + - Filter1 + update_time: '2021-05-11' + versions: 9 +- create_time: '2021-04-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: adf5e8bead686341 + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=adf5e8bead686341 + name: PepQuery Workflow for PXD023521 and PXD022296 COVID-19 Peptide Validation + May 2021 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - pepquery + - Grouping1 + - Filter1 + update_time: '2021-05-10' + versions: 7 +- create_time: '2021-05-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8bb3bc745ea62bed + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=8bb3bc745ea62bed + name: PepQuery Workflow for PXD025214 COVID-19 Peptide Validation May 2021 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - pepquery + - Grouping1 + - Filter1 + update_time: '2021-05-10' + versions: 4 +- create_time: '2020-12-19' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: b73fa5f8c0403454 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454 + name: Dataset collection PXD022085 Workflow for PQ and LK 12202020 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - query_tabular + - pepquery + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - Grep1 + - peptide_shaker + - search_gui + - msconvert + - Filter1 + update_time: '2021-05-04' + versions: 4 +- create_time: '2021-04-19' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 17a1433d0b681d4a + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=17a1433d0b681d4a + name: PepQuery Workflow for PXD023521 and PXD022296 COVID-19 Peptide Validation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - query_tabular + - pepquery + - Grouping1 + - unipept + update_time: '2021-04-30' + versions: 8 +- create_time: '2021-04-24' + creators: [] + doi: '' + edam_operation: + - Validation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ddd604341afd9cf7 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=ddd604341afd9cf7 + name: Strelka MIRACUM - main + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MIRACUM + tools: + - trimmomatic + - vcfcombine + - strelka_somatic + - qualimap_bamqc + - multiqc + - bwa_mem + update_time: '2021-04-29' + versions: 4 +- create_time: '2021-04-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7c80cd57b2de54d4 + latest_version: 22 + license: null + link: https://usegalaxy.eu/published/workflow?id=7c80cd57b2de54d4 + name: Spawn of Daughter of Blastn + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - table_compute + - tp_split_on_column + - collapse_dataset + - fasta2tab + - join1 + - tab2fasta + - trimmer + - ncbi_blastn_wrapper + - ncbi_makeblastdb + - Filter1 + update_time: '2021-04-28' + versions: 22 +- create_time: '2021-04-25' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 836cc09d17eaecb0 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=836cc09d17eaecb0 + name: Exploring Iris dataset with statistics and scatterplots + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - ggplot2_point + - bg_uniq + update_time: '2021-04-25' + versions: 1 +- create_time: '2021-04-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 65612d13b50547c8 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=65612d13b50547c8 + name: BLAST to BED + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - Add_a_column1 + - tp_cut_tool + - cat1 + - addValue + - Filter1 + update_time: '2021-04-24' + versions: 1 +- create_time: '2021-03-23' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: d70dc4cfeedb690b + latest_version: 33 + license: null + link: https://usegalaxy.eu/published/workflow?id=d70dc4cfeedb690b + name: scRNA Plant Analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - transcriptomics + - single-cell + tools: + - anndata_manipulate + - scanpy_filter + - scanpy_cluster_reduce_dimension + - scanpy_normalize + - scanpy_remove_confounders + - scanpy_plot + - anndata_import + - scanpy_inspect + update_time: '2021-04-24' + versions: 33 +- create_time: '2021-04-22' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Phylogenetic tree generation (from molecular sequences) + edam_topic: [] + id: d07fe8b5a045c176 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=d07fe8b5a045c176 + name: phylogeny + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_blastp_wrapper + - ncbi_acc_download + - muscle + - fasttree + - tp_cut_tool + - ncbi_makeblastdb + update_time: '2021-04-23' + versions: 4 +- create_time: '2021-04-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e66502f92a7d432b + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=e66502f92a7d432b + name: SPRING Mapping + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - spring_map + - split_file_to_collection + - collapse_dataset + update_time: '2021-04-23' + versions: 9 +- create_time: '2020-05-29' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 0882300f7b399587 + latest_version: 21 + license: null + link: https://usegalaxy.eu/published/workflow?id=0882300f7b399587 + name: Tetrahymena Mapping-by-Sequencing Full Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Tetrahymena + - Mapping-by-sequencing + tools: + - fastp + - tp_text_file_with_recurring_lines + - vcfvcfintersect + - mimodd_rebase + - mimodd_vcf_filter + - __ZIP_COLLECTION__ + - mimodd_map + - mimodd_info + - __RELABEL_FROM_FILE__ + - snpEff + - __BUILD_LIST__ + - bowtie2 + update_time: '2021-04-17' + versions: 21 +- create_time: '2021-04-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d7ae1144d942faf7 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=d7ae1144d942faf7 + name: MIRACUM - Prepare annotation data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - MIRACUM + tools: + - __APPLY_RULES__ + update_time: '2021-04-15' + versions: 1 +- create_time: '2021-04-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Visualisation + - Read summarisation + - Transcriptome assembly + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 68e8042f11d5a3fd + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=68e8042f11d5a3fd + name: APE_Souris_Abundance_Analyse_diff_RAEG + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - join1 + - ggplot2_pca + - tp_replace_in_column + - featurecounts + - hisat2 + - Remove beginning1 + - tp_sort_header_tool + - stringtie + - ggplot2_heatmap2 + - multiqc + - deseq2 + - table_compute + - Add_a_column1 + - tp_cat + - tp_cut_tool + - volcanoplot + - ggplot2_point + - tp_multijoin_tool + - Filter1 + update_time: '2021-04-10' + versions: 0 +- create_time: '2020-11-23' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 58db3e1996a8f093 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=58db3e1996a8f093 + name: Workflow for PXD021328 COVID-19 Peptide Validation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_blastp_wrapper + - Cut1 + - query_tabular + - pepquery + - Grouping1 + - tab2fasta + - unipept + update_time: '2021-04-07' + versions: 3 +- create_time: '2020-04-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: adc6d049e9283789 + latest_version: 12 + license: null + link: https://usegalaxy.eu/published/workflow?id=adc6d049e9283789 + name: Protein-ligand HTMD simulation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + - moleculardynamics + tools: + - get_pdb + - ambertools_acpype + - gmx_sim + - gmx_editconf + - gmx_em + - gmx_setup + - tp_grep_tool + - gmx_solvate + - gmx_merge_topology_files + - openbabel_compound_convert + update_time: '2021-04-06' + versions: 12 +- create_time: '2021-03-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2d2d0c2231babc50 + latest_version: 25 + license: null + link: https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50 + name: DE one-factor miRNA-mRNA target prediction + number_of_steps: null + source: https://usegalaxy.eu + tags: + - transcriptomics + - mirna + - arabidopsis + tools: + - fastqc + - Cut1 + - tp_sort_header_tool + - filter_by_fasta_ids + - trim_galore + - bg_uniq + - salmon + - tp_cut_tool + - rbc_mirdeep2_quantifier + - rbc_mirdeep2_mapper + - tp_find_and_replace + - targetfinder + - multiqc + - __MERGE_COLLECTION__ + - deseq2 + - Filter1 + update_time: '2021-04-01' + versions: 25 +- create_time: '2021-03-30' + creators: [] + doi: '' + edam_operation: + - Genome assembly + edam_topic: [] + id: cbe3769f1abb9fa5 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5 + name: Shovill and SISTR version 1.1.1 with final summary report + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Salmonella + - serotyping + - Illumina + - raw + - reads + tools: + - tp_cat + - shovill + - sistr_cmd + update_time: '2021-03-30' + versions: 3 +- create_time: '2021-03-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Visualisation + - Taxonomic classification + - Genome assembly + - Sequence composition calculation + - Aggregation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: b2b46e71046b1999 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999 + name: Workflow NGS Analysis (new) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - staramr_search + - trimmomatic + - quast + - Kraken2Tax + - taxonomy_krona_chart + - unicycler + - kraken2 + update_time: '2021-03-25' + versions: 2 +- create_time: '2021-03-18' + creators: + - Mehmet Tekman + doi: '' + edam_operation: [] + edam_topic: [] + id: 30623c815283da67 + latest_version: 9 + license: GPL-3.0-or-later + link: https://usegalaxy.eu/published/workflow?id=30623c815283da67 + name: Relabel headers in a collection with random names + number_of_steps: null + source: https://usegalaxy.eu + tags: + - 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RNA-Seq analysis + - Annotation + edam_topic: [] + id: 2f7c04ad219a9d2d + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=2f7c04ad219a9d2d + name: RNA-seq tutorial_2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - annotatemyids + - limma_voom + update_time: '2021-01-28' + versions: 0 +- create_time: '2021-01-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3a178ff6884a5d6d + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=3a178ff6884a5d6d + name: GTN Proteogemics3 Novel Peptide Analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:GalaxyP + - name:Proteogenomics + - name:GTN + tools: + - query_tabular + - ncbi_blastp_wrapper + - peptide_genomic_coordinate + - pep_pointer + update_time: '2021-01-27' + versions: 2 +- create_time: '2021-01-27' + creators: [] + doi: '' + edam_operation: + - Variant calling + - RNA-Seq analysis + - Transcriptome assembly + - 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tp_sort_header_tool + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2021-01-15' + versions: 0 +- create_time: '2021-01-15' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: bd74a116e3f8d5b8 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=bd74a116e3f8d5b8 + name: Calidad de las lecturas de un fichero FASTQ + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2021-01-15' + versions: 0 +- create_time: '2020-10-13' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 3676aafc35dc2fe7 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7 + name: EncyclopeDIA Standard Workflow 64Intensity + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - encyclopedia_quantify + - encyclopedia_searchtolib + - msconvert + update_time: '2021-01-15' + versions: 5 +- create_time: '2021-01-12' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Sequence trimming + - Read summarisation + - RNA-Seq quantification + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Primer removal + edam_topic: [] + id: d72edb9f8c529f47 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=d72edb9f8c529f47 + name: Pseudogene DEG By Amir Sabbaghian(Paired END) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - trim_galore + - hisat2 + - featurecounts + - deseq2 + - Filter1 + update_time: '2021-01-12' + versions: 3 +- create_time: '2021-01-07' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 77e85bde57477194 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=77e85bde57477194 + name: Answer Workflow - Clustering 3k PBMC + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - anndata_manipulate + - scanpy_filter + - anndata_inspect + - Cut1 + - scanpy_inspect + - scanpy_cluster_reduce_dimension + - scanpy_normalize + - tp_replace_in_column + - tp_tail_tool + - tp_awk_tool + - cat1 + - scanpy_plot + - anndata_import + - scanpy_remove_confounders + - Filter1 + update_time: '2021-01-07' + versions: 1 +- create_time: '2020-04-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 01274dfdbdfcaa88 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=01274dfdbdfcaa88 + name: Workflow constructed from history 'STOC CSI' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - stoceps_trend_indic + - stoceps_maketablecarrer + - stoceps_filteringsp + - stoceps_glm + update_time: '2021-01-06' + versions: 1 +- create_time: '2021-01-06' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2a39dbc8fc6dd5d3 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=2a39dbc8fc6dd5d3 + name: 'COVID-19: Variation analysis for PE RNASeq Illumina data' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID19 + - RNASeq + - PE + - Illumina + - Fastq->VCF + tools: + - fastp + - multiqc + - Cut1 + - collapse_dataset + - lofreq_call + - lofreq_indelqual + - tp_grep_tool + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - __FILTER_FROM_FILE__ + - picard_MarkDuplicates + - samtools_view + - Filter1 + - lofreq_viterbi + - bwa_mem + update_time: '2021-01-06' + versions: 1 +- create_time: '2020-12-15' + creators: [] + doi: '' + edam_operation: + - Formatting + - Read mapping + edam_topic: [] + id: 93e32219d412c1f1 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=93e32219d412c1f1 + name: GATK4 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - gatk4_mutect2 + - picard_SortSam + - picard_AddOrReplaceReadGroups + - picard_MarkDuplicates + - bowtie2 + update_time: '2021-01-02' + versions: 3 +- create_time: '2020-12-15' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: 231a2dc7412d250b + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=231a2dc7412d250b + name: VARSCAN2 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - samtools_sort + - varscan_mpileup + - samtools_view + - samtools_mpileup + - bowtie2 + update_time: '2021-01-02' + versions: 4 +- create_time: '2020-12-15' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: 1d41197b6c664b68 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=1d41197b6c664b68 + name: SAMTools + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - samtools_view + - samtools_sort + - bowtie2 + - samtools_mpileup + update_time: '2021-01-01' + versions: 3 +- create_time: '2020-12-28' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: bfe26679d670bb5e + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=bfe26679d670bb5e + name: MGF INPUTS Workflow for COVID-19 Peptide Validation PXD021328 12282020 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - query_tabular + - pepquery + - Grouping1 + - unipept + - Filter1 + update_time: '2020-12-28' + versions: 3 +- create_time: '2020-12-16' + creators: [] + doi: '' + edam_operation: + - Filtering + - Visualisation + - Prediction and recognition + - Formatting + edam_topic: [] + id: 02700454f57eb556 + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=02700454f57eb556 + name: Workflow for COVID-19 Peptide Validation PXD018094 and PXD022085 and PXD020394 + 12202020 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - query_tabular + - pepquery + - Grouping1 + - unipept + - msconvert + - Filter1 + update_time: '2020-12-21' + versions: 11 +- create_time: '2020-12-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Genome assembly + - Sequence composition calculation + - Read mapping + - Coding region prediction + - Validation + - Genome annotation + - Visualisation + - Gene prediction + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 7aa32aba3fde0708 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708 + name: 'Genome Assembly of MRSA using Illumina MiSeq data ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - staramr_search + - trimmomatic + - quast + - CONVERTER_bz2_to_uncompressed + - shovill + - bandage_image + - prokka + - jbrowse + - multiqc + - bowtie2 + update_time: '2020-12-17' + versions: 1 +- create_time: '2020-12-17' + creators: [] + doi: '' + edam_operation: + - 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ct_combine_tool_outputs + - garnett_classify_cells + - monocle3_create + update_time: '2020-12-07' + versions: 0 +- create_time: '2020-12-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8c44228d11782e61 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8c44228d11782e61 + name: Workflow 'Nik Galaxy 101' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2020-12-07' + versions: 1 +- create_time: '2020-12-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 61dcc0998fa4d309 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=61dcc0998fa4d309 + name: automatically extracted WF of Martin + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2020-12-07' + versions: 1 +- create_time: '2020-08-19' + creators: [] + doi: '' + edam_operation: + - 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assembly + tools: + - nanoplot + - quast + - staramr_search + - tbl2gff3 + - flye + - CONVERTER_bz2_to_uncompressed + - filtlong + - prokka + - Grep1 + - jbrowse + - bandage_image + update_time: '2020-12-03' + versions: 6 +- create_time: '2020-11-30' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + - Sequencing quality control + edam_topic: [] + id: 08cfb9b21c1ec808 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808 + name: STRT-Seq Workflow (with barcodes) (rename sequences) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - umi_tools_extract + - umi_tools_count + - rna_star + - umi_tools_dedup + - featurecounts + - cshl_fastx_renamer + update_time: '2020-11-30' + versions: 3 +- create_time: '2020-11-30' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + - Sequencing quality control + edam_topic: [] + id: d4b3da4cc5a50044 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=d4b3da4cc5a50044 + name: STRT-Seq Workflow (no barcodes) (rename sequences) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - umi_tools_extract + - umi_tools_count + - rna_star + - umi_tools_dedup + - featurecounts + - cshl_fastx_renamer + update_time: '2020-11-30' + versions: 8 +- create_time: '2020-11-30' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Mapping + edam_topic: [] + id: d4a6fb334f5dd10e + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=d4a6fb334f5dd10e + name: FLAIR-workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - minimap2 + - flair_correct + - bedtools_bamtobed + - flair_collapse + update_time: '2020-11-30' + versions: 2 +- create_time: '2020-10-03' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 1809fcaec264eac9 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9 + name: Dataset collection PXD020394 Workflow for PQ and LK 10032020 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - 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cat1 + - gops_intersect_1 + - Filter1 + update_time: '2020-11-20' + versions: 0 +- create_time: '2020-11-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 409ac72c9906f16a + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=409ac72c9906f16a + name: Removing cells expressing a gene + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - column_remove_by_header + - table_compute + - anndata_manipulate + - anndata_inspect + update_time: '2020-11-19' + versions: 3 +- create_time: '2020-11-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9668976304efea5c + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=9668976304efea5c + name: Filter FASTQ on BAM File and Capture Regions + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - samtools_view + - seq_filter_by_mapping + update_time: '2020-11-19' + versions: 3 +- create_time: '2020-01-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: bcec217b62ccc7af + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af + name: Atlas-Scanpy-SCMap + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scmap_preprocess_sce + - scanpy_find_cluster + - scanpy_scale_data + - scanpy_read_10x + - scanpy_run_pca + - scanpy_compute_graph + - sceasy_convert + - scanpy_normalise_data + - scmap_scmap_cluster + - scanpy_filter_cells + - scanpy_filter_genes + - scmap_scmap_cell + - scanpy_find_variable_genes + - retrieve_scxa + update_time: '2020-11-05' + versions: 3 +- create_time: '2020-11-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 66834f10c86362b9 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=66834f10c86362b9 + name: RNA-RNA interactome analysis using CLAN + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - transcriptomics + tools: + - fastqc + - chira_quantify + - chira_collapse + - query_tabular + - chira_extract + - cutadapt + - chira_map + - 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moleculardynamics + tools: + - gmx_trj + update_time: '2020-10-30' + versions: 2 +- create_time: '2019-07-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 71f7725b261c6c83 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83 + name: HumanCellAtlas-Scanpy-CellBrowser + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_find_cluster + - scanpy_scale_data + - scanpy_read_10x + - scanpy_compute_graph + - scanpy_find_markers + - ucsc_cell_browser + - scanpy_normalise_data + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - hca_matrix_downloader + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2020-10-26' + versions: 3 +- create_time: '2020-10-06' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 229a955d29bd4064 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=229a955d29bd4064 + name: PXD020394 NEGATIVE/POSITIVE Species SG/PS PQ for Metaproteomics 10082020 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - unipept + - Remove beginning1 + - Cut1 + - query_tabular + - pepquery + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - cat1 + - Grep1 + - uniprotxml_downloader + - peptide_shaker + - dbbuilder + - search_gui + - Filter1 + update_time: '2020-10-09' + versions: 8 +- create_time: '2020-10-06' + creators: [] + doi: '' + edam_operation: + - Filtering + - Visualisation + - Prediction and recognition + - Formatting + edam_topic: [] + id: 6cb85fe1ad0c9f3b + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b + name: 'imported: PXD020394 Metaproteomics Workflow 10062020' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - unipept + - Remove beginning1 + - Cut1 + - query_tabular + - pepquery + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - cat1 + - Grep1 + - uniprotxml_downloader + - peptide_shaker + - dbbuilder + - search_gui + - msconvert + - Filter1 + update_time: '2020-10-06' + versions: 1 +- create_time: '2020-05-16' + creators: [] + doi: '' + edam_operation: + - Parsing + - Image analysis + - Quantification + edam_topic: [] + id: 4a41ea1eb6752171 + latest_version: 70 + license: null + link: https://usegalaxy.eu/published/workflow?id=4a41ea1eb6752171 + name: CP_pipeline_IDR_training + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CellProfiler + - CellProfiler + tools: + - cp_measure_object_intensity + - cp_measure_object_size_shape + - cp_image_math + - cp_enhance_or_suppress_features + - cp_gray_to_color + - cp_convert_objects_to_image + - cp_mask_image + - cp_measure_texture + - idr_download_by_ids + - cp_measure_image_area_occupied + - cp_save_images + - cp_identify_primary_objects + - cp_cellprofiler + - cp_measure_image_quality + - cp_common + - cp_export_to_spreadsheet + - cp_measure_image_intensity + - cp_relate_objects + - cp_display_data_on_image + - cp_measure_granularity + update_time: '2020-10-05' + versions: 70 +- create_time: '2020-09-24' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 5dec0e5a2d75cdc1 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1 + name: EncycopeDIA Standard Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - encyclopedia_quantify + - encyclopedia_searchtolib + - msconvert + update_time: '2020-10-02' + versions: 2 +- create_time: '2020-01-22' + creators: [] + doi: '' + edam_operation: + - Sequencing quality control + - Filtering + - Box-Whisker plot plotting + - Scatter plot plotting + edam_topic: [] + id: c3bfedf33bb00069 + latest_version: 14 + license: null + link: https://usegalaxy.eu/published/workflow?id=c3bfedf33bb00069 + name: Avans QC + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Avans + - Nanopore + tools: + - nanoplot + - filtlong + update_time: '2020-10-01' + versions: 14 +- create_time: '2020-06-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e97bdba3834ac465 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=e97bdba3834ac465 + name: EBI SC Expression Atlas Release 11 Analysis Pipeline (Scanpy 1.4.3) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_find_variable_genes + - scanpy_find_cluster + - scanpy_plot_embed + - scanpy_read_10x + - scanpy_compute_graph + - scanpy_find_markers + - _ensembl_gtf2gene_list + - scanpy_normalise_data + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_parameter_iterator + - scanpy_run_pca + update_time: '2020-09-30' + versions: 0 +- create_time: '2020-09-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 470b629d22b0fc51 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=470b629d22b0fc51 + name: SARS-CoV-2 PepQuery Validation + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - pepquery + update_time: '2020-09-21' + versions: 0 +- create_time: '2020-09-11' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Sequence alignment analysis + - Data handling + - Genome assembly + - Local alignment + - Read mapping + - Global alignment + - Sequence contamination filtering + - Sequence analysis + - Sequence file editing + - Sequence assembly visualisation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 93d1035a307fe63d + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d + name: Copy of LSDV Assembly + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastp + - 'EMBOSS: megamerger53' + - bandage_info + - filter_by_fasta_ids + - ncbi_acc_download + - spades + - fasta_merge_files_and_filter_unique_sequences + - seqtk_mergefa + - samtools_stats + - jbrowse + - CONVERTER_bam_to_bigwig_0 + - rseqc_bam_stat + - bandage_image + - deeptools_bam_coverage + - bowtie2 + update_time: '2020-09-11' + versions: 0 +- create_time: '2020-07-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 48759b33146f9583 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=48759b33146f9583 + name: 'SARS-CoV-2: downsample ONT reads assigned to transcripts' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ONT + - covid19.galaxyproject.org + tools: + - samtools_view + update_time: '2020-09-07' + versions: 8 +- create_time: '2020-08-22' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: d5756e3ebfa285ef + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef + name: Dataset collection PXD018241 Workflow for PQ and LK 09022020 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - query_tabular + - pepquery + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - Grep1 + - peptide_shaker + - search_gui + - msconvert + - Filter1 + update_time: '2020-09-03' + versions: 11 +- create_time: '2020-08-22' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 4c81726bde25c36a + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a + name: Dataset collection PXD018804 Workflow for PQ and LK 08222020 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - query_tabular + - pepquery + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - Grep1 + - peptide_shaker + - search_gui + - msconvert + - Filter1 + update_time: '2020-09-01' + versions: 3 +- create_time: '2020-07-14' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Formatting + edam_topic: [] + id: 1b38e0d69e366be1 + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=1b38e0d69e366be1 + name: 'SARS-CoV-2: map ONT reads to transcripts' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ONT + - covid19.galaxyproject.org + tools: + - samtools_fastx + - picard_NormalizeFasta + - filter_by_fasta_ids + - minimap2 + - samtools_view + - deeptools_bam_coverage + update_time: '2020-08-30' + versions: 7 +- create_time: '2020-08-28' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 7f76e43f19b27b22 + latest_version: 12 + license: null + link: https://usegalaxy.eu/published/workflow?id=7f76e43f19b27b22 + name: 'SARS-CoV-2: classify ONT reads by transcript junction' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - ONT + - covid19.galaxyproject.org + tools: + - tp_text_file_with_recurring_lines + - Cut1 + - split_file_to_collection + - collapse_dataset + - __BUILD_LIST__ + - __RELABEL_FROM_FILE__ + - cat1 + - bedtools_intersectbed + - tp_head_tool + - tp_replace_in_column + - samtools_view + - param_value_from_file + - __MERGE_COLLECTION__ + - createInterval + update_time: '2020-08-30' + versions: 12 +- create_time: '2020-05-24' + creators: [] + doi: '' + edam_operation: + - Community profiling + - Sequence alignment + - Loading + edam_topic: [] + id: d79309343e2a5d62 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=d79309343e2a5d62 + name: 10X StarSolo Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: + - transcriptomics + - single-cell + tools: + - cat1 + - rna_starsolo + - dropletutils + update_time: '2020-08-22' + versions: 3 +- create_time: '2020-07-20' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Visualisation + - Taxonomic classification + - Box-Whisker plot plotting + - Scatter plot plotting + edam_topic: [] + id: 57cfe5062c8e01bf + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=57cfe5062c8e01bf + name: PARE-Seq_ARGs_Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - nanoplot + - taxonomy_krona_chart + - Cut1 + - tp_replace_in_line + - join1 + - mergeCols1 + - kraken2 + - datamash_reverse + - minimap2 + update_time: '2020-08-03' + versions: 4 +- create_time: '2020-07-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7c45c90fffe40aca + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=7c45c90fffe40aca + name: Population and community metrics calculation from Biodiversity data + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Community_metrics + - Presence_absence + - GLM + tools: + - pampa_glmcomm + - pampa_presabs + - pampa_glmsp + - pampa_communitymetrics + update_time: '2020-07-24' + versions: 3 +- create_time: '2020-07-23' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: f774cf05ddff3612 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=f774cf05ddff3612 + name: Workflow with Copernicus Essential Climate Variable - select and plot + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - xarray_metadata_info + - Add_a_column1 + - datamash_ops + - cds_essential_variability + - tp_awk_tool + - ggplot2_point + - xarray_select + update_time: '2020-07-23' + versions: 3 +- create_time: '2020-07-15' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: c750484145c9903b + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=c750484145c9903b + name: PXD018594_workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_cat + - msms_extractor + - Grep1 + - peptide_shaker + - search_gui + - msconvert + - Show beginning1 + update_time: '2020-07-16' + versions: 4 +- create_time: '2020-06-10' + creators: [] + doi: '' + edam_operation: + - Filtering + - Formatting + edam_topic: [] + id: 6b7b86756060659b + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=6b7b86756060659b + name: SEARCH PXD018804 WORKFLOW + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - peptide_shaker + - msms_extractor + - msconvert + - search_gui + update_time: '2020-07-16' + versions: 6 +- create_time: '2020-06-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c6008842e3788bfc + latest_version: 19 + license: null + link: https://usegalaxy.eu/published/workflow?id=c6008842e3788bfc + name: 'SARS-CoV-2: ONT-Tombo-sample-Compare' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid-19 + - name:ONT + - name:DRS + - name:publish + tools: + - tombo_text_output + - tombo_detect_modifications + update_time: '2020-07-14' + versions: 19 +- create_time: '2020-07-04' + creators: [] + doi: '' + edam_operation: + - k-mer counting + - PolyA signal detection + - Post-translation modification site prediction + - Genotyping + edam_topic: [] + id: 778923dd04996e07 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=778923dd04996e07 + name: 'SARS-CoV-2: ONT-NanoCompore-SampComp 3-replicates' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid-19 + - name:ONT + - name:DRS + - name:publish + tools: + - nanocompore_db + - nanocompore_sampcomp + update_time: '2020-07-14' + versions: 6 +- create_time: '2020-06-12' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + edam_topic: [] + id: 1e2d27fae8a41ac1 + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1 + name: 'EBI-Training: scRNA - From fastq to Anndata' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - dropletutils_read_10x + - sceasy_convert + - _dropletBarcodePlot + - dropletutils_empty_drops + update_time: '2020-07-14' + versions: 9 +- create_time: '2020-07-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c817aefc77933d79 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=c817aefc77933d79 + name: 'Workflow 3: Functional Information [Metatranscriptomics]' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - metagenomics + tools: + - humann2_unpack_pathways + - humann2_renorm_table + - group_humann2_uniref_abundances_to_go + - humann2 + update_time: '2020-07-14' + versions: 1 +- create_time: '2020-06-19' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + edam_topic: [] + id: e271d95a671182ec + latest_version: 16 + license: null + link: https://usegalaxy.eu/published/workflow?id=e271d95a671182ec + name: 'SARS-CoV-2: IVT reads filter, sample, alignment' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid-19 + - name:ONT + - name:DRS + - name:publish + tools: + - samtools_fastx + - fastq_filter + - split_file_to_collection + - samtools_merge + - tp_cat + - Cut1 + - minimap2 + - samtools_view + - ont_fast5_api_fast5_subset + update_time: '2020-07-10' + versions: 16 +- create_time: '2020-06-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 01c8b37da702ada6 + latest_version: 35 + license: null + link: https://usegalaxy.eu/published/workflow?id=01c8b37da702ada6 + name: 'SARS-CoV-2: ONT-Tombo-Methylation' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid-19 + - name:ONT + - name:DRS + tools: + - tombo_text_output + - tombo_resquiggle + - tombo_detect_modifications + update_time: '2020-07-08' + versions: 35 +- create_time: '2020-06-03' + creators: [] + doi: '' + edam_operation: + - k-mer counting + - PolyA signal detection + - Methylation analysis + - Post-translation modification site prediction + - Collapsing methods + - Genotyping + edam_topic: [] + id: 77db45ad90b4033d + latest_version: 28 + license: null + link: https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d + name: 'SARS-CoV-2: ONT-NanoCompore-Methylation-transcripts' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid-19 + - name:ONT + - name:DRS + tools: + - nanocompore_db + - nanopolish_eventalign + - nanopolishcomp_eventaligncollapse + - tp_awk_tool + - nanocompore_sampcomp + update_time: '2020-07-08' + versions: 28 +- create_time: '2020-02-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Read summarisation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 94bbf8fa7c1f030d + latest_version: 29 + license: null + link: https://usegalaxy.eu/published/workflow?id=94bbf8fa7c1f030d + name: Single RNASeq Primary Analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - tp_sort_header_tool + - stringtie + - rna_star + - multiqc + - featurecounts + - Filter1 + update_time: '2020-07-03' + versions: 29 +- create_time: '2020-06-29' + creators: [] + doi: '' + edam_operation: + - Community profiling + - Sequence alignment + - Loading + edam_topic: [] + id: 7d22eea4278570e8 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=7d22eea4278570e8 + name: Parallel STARSolo + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ralf + tools: + - anndata_manipulate + - rna_starsolo + - dropletutils + - anndata_import + update_time: '2020-06-30' + versions: 4 +- create_time: '2020-06-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ebe7fbc738f4af42 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=ebe7fbc738f4af42 + name: Pre-MT2MQ Functional Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - humann2_rename_table + - humann2_regroup_table + - humann2_renorm_table + - humann2_join_tables + update_time: '2020-06-30' + versions: 1 +- create_time: '2020-06-03' + creators: [] + doi: '' + edam_operation: + - Mapping + - Formatting + - Pairwise sequence alignment + edam_topic: [] + id: 82a60d94d699efbf + latest_version: 28 + license: null + link: https://usegalaxy.eu/published/workflow?id=82a60d94d699efbf + name: 'SARS-CoV-2: Assign ONT reads to transcripts' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid-19 + - name:ONT + - name:DRS + tools: + - samtools_fastx + - picard_NormalizeFasta + - filter_by_fasta_ids + - samtools_merge + - Cut1 + - deeptools_bam_coverage + - bedtools_intersectbed + - minimap2 + - samtools_view + - __BUILD_LIST__ + - createInterval + update_time: '2020-06-29' + versions: 28 +- create_time: '2020-06-29' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Community profiling + - Sequence alignment + - Loading + edam_topic: [] + id: b5627201bb4f6943 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=b5627201bb4f6943 + name: STARsolo and Scanpy Workflow constructed from history 'single-cell share''' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ralf + tools: + - scanpy_filter + - rna_starsolo + - dropletutils + - anndata_import + update_time: '2020-06-29' + versions: 1 +- create_time: '2020-04-27' + creators: [] + doi: '' + edam_operation: + - Read mapping + - Genetic variation analysis + edam_topic: [] + id: c3f2350f0be2d9c9 + latest_version: 23 + license: null + link: https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9 + name: 'COVID-19: Neo-antigen prediction.' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - iedb_api + - seq2hla + - custom_pro_db + update_time: '2020-06-25' + versions: 23 +- create_time: '2020-06-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Aggregation + - Coding region prediction + - Validation + - Sequence contamination filtering + - Genome annotation + - Visualisation + - Gene prediction + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 374797e58377c40f + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=374797e58377c40f + name: 0_Short-read_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Assembly + - Unicycler + - StarAMR + - Bacterial + - Prokka + - Short-Read + - Illumina + tools: + - fastqc + - fastp + - quast + - staramr_search + - bandage_info + - unicycler + - bandage_image + - prokka + - multiqc + update_time: '2020-06-24' + versions: 4 +- create_time: '2020-06-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Aggregation + - Coding region prediction + - Pairwise sequence alignment + - Genome annotation + - Box-Whisker plot plotting + - Filtering + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + - Genome assembly + - Sequence composition calculation + - Mapping + - Validation + - Sequence contamination filtering + - Visualisation + - Gene prediction + - Scatter plot plotting + edam_topic: [] + id: ecf48fa50af560a0 + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0 + name: 0_Hybrid_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Hybrid + - Assembly + - ONT + - Unicycler + - StarAMR + - Bacterial + - Prokka + tools: + - fastqc + - nanoplot + - fastp + - quast + - staramr_search + - bandage_info + - Cut1 + - bedtools_genomecoveragebed + - unicycler + - bandage_image + - filtlong + - prokka + - Summary_Statistics1 + - minimap2 + - multiqc + update_time: '2020-06-24' + versions: 13 +- create_time: '2020-06-24' + creators: [] + doi: '' + edam_operation: + - Sequencing quality control + - Genome assembly + - Mapping + - Aggregation + - Coding region prediction + - Pairwise sequence alignment + - Genome annotation + - Visualisation + - Box-Whisker plot plotting + - Gene prediction + - Filtering + - Sequence assembly visualisation + - Sequence assembly validation + - Scatter plot plotting + edam_topic: [] + id: ea485dbabc76488d + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d + name: 0_Long-read_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Assembly + - ONT + - Unicycler + - StarAMR + - Bacterial + - Prokka + - Coverage + tools: + - nanoplot + - quast + - staramr_search + - bandage_info + - Cut1 + - bedtools_genomecoveragebed + - unicycler + - filtlong + - prokka + - Summary_Statistics1 + - minimap2 + - bandage_image + update_time: '2020-06-24' + versions: 3 +- create_time: '2019-04-11' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: 64bb7a64877034dc + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc + name: Co-registration of MSI image and real image with landmarks + number_of_steps: null + source: https://usegalaxy.eu + tags: + - massspectrometryimaging + tools: + - Remove beginning1 + - addName + - imagecoordinates_flipaxis + - tp_cat + - ip_landmark_registration + - graphicsmagick_image_convert + - ip_coordinates_of_roi + - ip_projective_transformation_points + - ip_scale_image + - ip_viz_overlay_moving_and_fixed_image + update_time: '2020-06-22' + versions: 11 +- create_time: '2020-06-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d5b1fab611ddfeb0 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=d5b1fab611ddfeb0 + name: 'SARS-CoV-2: ONT viral reads preprocess fast5s ' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - name:covid-19 + - name:ONT + - name:DRS + tools: + - ont_fast5_api_fast5_subset + - ont_fast5_api_compress_fast5 + - ont_fast5_api_multi_to_single_fast5 + update_time: '2020-06-19' + versions: 6 +- create_time: '2020-04-18' + creators: [] + doi: '' + edam_operation: + - Formatting + - Data handling + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b02d90c32dc67730 + latest_version: 21 + license: null + link: https://usegalaxy.eu/published/workflow?id=b02d90c32dc67730 + name: 'COVID-19: GATK4' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - samtools_fastx + - vcfallelicprimitives + - fastp + - gatk4_mutect2 + - picard_SortSam + - snpSift_extractFields + - fasterq_dump + - picard_AddOrReplaceReadGroups + - cat1 + - snpEff_build_gb + - snpEff + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + - bwa_mem + update_time: '2020-06-18' + versions: 21 +- create_time: '2020-06-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5fae484cb18b94e2 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=5fae484cb18b94e2 + name: Download and SE+PE Illumina Covid Variation Workflow (EU version) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - __MERGE_COLLECTION__ + - collapse_dataset + update_time: '2020-06-11' + versions: 6 +- create_time: '2020-06-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Sequence trimming + - Visualisation + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 02655d0e4af0ee0d + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d + name: ATAC-seq GTM with control and macs2 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - atac-seq + tools: + - fastqc + - deeptools_plot_heatmap + - bedtools_bamtobed + - samtools_sort + - deeptools_compute_matrix + - bamFilter + - pygenomeTracks + - bedtools_sortbed + - cutadapt + - picard_CollectInsertSizeMetrics + - genrich + - tp_awk_tool + - macs2_callpeak + - wig_to_bigWig + - picard_MarkDuplicates + - bowtie2 + update_time: '2020-06-10' + versions: 3 +- create_time: '2020-05-22' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Genome assembly + - Mapping assembly + - De-novo assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: b4de76c0a4d0e23a + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a + name: Nanopore v1.1 / Minimap2, Miniasm, Racon + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - nanoplot + - trimmomatic + - staramr_search + - PlasFlow + - racon + - miniasm + - gfa_to_fa + - minimap2 + - bandage_image + - fastq_groomer + update_time: '2020-06-10' + versions: 3 +- create_time: '2020-05-29' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 0d7c643d7720ee31 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=0d7c643d7720ee31 + name: 'EBI-Tutorial 3: Filtering, Normalisation, and Batch Correction' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_scale_data + - scanpy_compute_graph + - scanpy_normalise_data + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_plot + - scanpy_regress_variable + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2020-05-29' + versions: 1 +- create_time: '2020-05-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a7fcfab658a2cc33 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a7fcfab658a2cc33 + name: 'EBI Tutorial 4: Dimensionality reduction and marker identification' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - monocle3_partition + - monocle3_plotCells + - monocle3_reduceDim + - monocle3_topmarkers + update_time: '2020-05-29' + versions: 1 +- create_time: '2020-05-29' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + edam_topic: [] + id: f944ad0c35d1a472 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472 + name: 'EBI-Tutorial 2: Droplet quantification and preprocessing' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - dropletutils_read_10x + - sceasy_convert + - cat1 + - _dropletBarcodePlot + - dropletutils_empty_drops + update_time: '2020-05-29' + versions: 1 +- create_time: '2020-05-24' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d7aa4c258e2edc95 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=d7aa4c258e2edc95 + name: Understanding Barcodes + number_of_steps: null + source: https://usegalaxy.eu + tags: + - transcriptomics + tools: + - fastqc + - seq_filter_by_id + - umi_tools_extract + update_time: '2020-05-24' + versions: 1 +- create_time: '2020-05-24' + creators: [] + doi: '' + edam_operation: + - Sequencing quality control + - Read pre-processing + - Sequence visualisation + edam_topic: [] + id: f055b8fa294d4be8 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f055b8fa294d4be8 + name: Single-Cell Quality Control with Scater + number_of_steps: null + source: https://usegalaxy.eu + tags: + - transcriptomics + - single-cell + tools: + - scater_plot_dist_scatter + - scater_plot_pca + - scater_filter + - scater_create_qcmetric_ready_sce + update_time: '2020-05-24' + versions: 1 +- create_time: '2020-05-23' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 848389c45cebe34f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=848389c45cebe34f + name: Clustering ML + number_of_steps: null + source: https://usegalaxy.eu + tags: + - statistics + - clustering + - ml + tools: + - ggplot2_point + - sklearn_numeric_clustering + - csv_to_tabular + update_time: '2020-05-23' + versions: 1 +- create_time: '2020-05-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 138d4893a1d6228e + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=138d4893a1d6228e + name: Regression ML + number_of_steps: null + source: https://usegalaxy.eu + tags: + - statistics + - regression + - 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Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: 0ab3e47ebd3b520e + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e + name: 'COVID-19: assembly using Tophat2 and annotation' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - glimmer_build-icm + - cuffquant + - cuffdiff + - fasterq_dump + - glimmer_knowlegde-based + - hmmer_jackhmmer + - cufflinks + - transdecoder + - uniprotxml_downloader + - multiqc + - fastp + - ncbi_blastp_wrapper + - antismash + - tophat2 + - ncbi_makeblastdb + - samtool_filter2 + - bwa_mem + - samtools_fastx + - gffread + - cuffmerge + update_time: '2020-05-06' + versions: 13 +- create_time: '2020-05-01' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7117dbcbd5d12de5 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=7117dbcbd5d12de5 + name: RNA-Seq-Trair10 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - qualimap_rnaseq + - rna_star + - fastq_groomer + update_time: '2020-05-05' + versions: 4 +- create_time: '2020-05-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 092d01f759659e6b + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=092d01f759659e6b + name: HTMD analysis with collections + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + - moleculardynamics + tools: + - bio3d_rmsf + - bio3d_rmsd + - bio3d_pca + - mdanalysis_cosine_analysis + - vmd_hbonds + - md_converter + - bio3d_pca_visualize + - gmx_editconf + update_time: '2020-05-04' + versions: 3 +- create_time: '2020-04-30' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 392a5d91ac221104 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=392a5d91ac221104 + name: Workflow constructed from history 'climate 101' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - datamash_ops + - cds_essential_variability + - Grep1 + - tp_awk_tool + - psy_maps + - ggplot2_point + - climate_stripes + update_time: '2020-04-30' + versions: 0 +- create_time: '2020-01-22' + creators: [] + doi: '' + edam_operation: + - Sequencing quality control + - Genome visualisation + - Taxonomic classification + - Genome assembly + - Multilocus sequence typing + - Coding region prediction + - Pairwise sequence alignment + - Genome annotation + - Visualisation + - Antimicrobial resistance prediction + - Box-Whisker plot plotting + - Mapping assembly + - Gene prediction + - Filtering + - Sequence assembly visualisation + - Sequence assembly validation + - Scatter plot plotting + edam_topic: [] + id: 5826e573b6f93762 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=5826e573b6f93762 + name: MetaGalaxy + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Long_Read + - Metagenomics + - Assembly + - AMR + - Taxonomy + - Gene_Annotation + - Long_Read + tools: + - nanoplot + - meta_flye + - abricate + - quast + - Cut1 + - bandage_info + - racon + - filtlong + - prokka + - kraken2 + - Krona + - mlst + - jbrowse + - minimap2 + - bandage_image + update_time: '2020-04-21' + versions: 1 +- create_time: '2020-04-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 182eb73befccb68c + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=182eb73befccb68c + name: XChem_combined-Public_test + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: [] + update_time: '2020-04-11' + versions: 3 +- create_time: '2020-04-09' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome assembly + edam_topic: [] + id: 9ba580ba8b01db40 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 + name: SARS-CoV-2 vBiohackathon workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - vg_deconstruct + - tp_cat + - minia + - __FILTER_FAILED_DATASETS__ + - seqwish + - minimap2 + - vg_convert + - vg_view + update_time: '2020-04-10' + versions: 8 +- create_time: '2020-04-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ec0d89aa1e6674e4 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=ec0d89aa1e6674e4 + name: test + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Add_a_column1 + - tp_find_and_replace + update_time: '2020-04-09' + versions: 1 +- create_time: '2020-04-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6ea9c7e45df94bf8 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=6ea9c7e45df94bf8 + name: 'Workflow constructed from history ''imported from archive: Aula 1''' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - join1 + - Grouping1 + - tp_cut_tool + update_time: '2020-04-04' + versions: 6 +- create_time: '2020-04-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 40a621934a07c7ee + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=40a621934a07c7ee + name: Workflow on read mapping with BWA + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - tp_sort_header_tool + - trim_galore + - bamFilter + - bwa + - samtools_flagstat + - deeptools_bam_coverage + update_time: '2020-04-03' + versions: 2 +- create_time: '2020-04-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6006e42ec358c785 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=6006e42ec358c785 + name: Protein-ligand docking (B2AR) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + tools: + - get_pdb + - prepare_box + - tp_grep_tool + - sdf_to_tab + - prepare_receptor + - docking + - openbabel_compound_convert + update_time: '2020-04-02' + versions: 5 +- create_time: '2020-03-29' + creators: [] + doi: '' + edam_operation: + - Sequence assembly visualisation + - Aggregation + - Genome assembly + edam_topic: [] + id: c702c76cadebac30 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=c702c76cadebac30 + name: ONT - Workflow-Wick-et.al. + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ONT + tools: + - bandage_image + - spades + - unicycler + - bandage_info + update_time: '2020-03-29' + versions: 2 +- create_time: '2019-05-20' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + edam_topic: [] + id: 44e16f0782f54111 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=44e16f0782f54111 + name: ONT -- Metagenomics-Kraken2-Krona + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ONT + tools: + - tp_replace_in_line + - kraken2 + - taxonomy_krona_chart + - datamash_reverse + update_time: '2020-03-29' + versions: 2 +- create_time: '2019-07-05' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + edam_topic: [] + id: 816815a93cc68244 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=816815a93cc68244 + name: ONT --Tutorial-Nanopolish-variants-upgraded + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ONT + - Nanopore + tools: + - minimap2 + - nanopolish_variants + update_time: '2020-03-29' + versions: 5 +- create_time: '2019-07-05' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Cross-assembly + - Mapping assembly + - De-novo assembly + - Aggregation + edam_topic: [] + id: b2dfa74f55a73409 + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409 + name: nanopolish_variants_with-flye-unicycler + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ONT + tools: + - minimap2 + - nanopolish_variants + - unicycler + - flye + update_time: '2020-03-29' + versions: 7 +- create_time: '2020-02-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Genome indexing + - Sequence composition calculation + - Read mapping + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Generation + - Sequencing quality control + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: 49ce9e738fadef4a + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=49ce9e738fadef4a + name: 'COVID-19: read pre-processing with download' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - picard_MergeSamFiles + - fasterq_dump + - minimap2 + - multiqc + - samtool_filter2 + - bwa_mem + update_time: '2020-03-29' + versions: 8 +- create_time: '2020-03-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cdf677a621166238 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=cdf677a621166238 + name: Find exons with the highest number of interactions + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2020-03-27' + versions: 1 +- create_time: '2020-03-24' + creators: [] + doi: '' + edam_operation: + - Data handling + - Sequence annotation + edam_topic: [] + id: 799b924edd3c401b + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=799b924edd3c401b + name: Franco_Metagenome_to_Metaproteomic_Db + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - metagene_annotator + - sixgill_build + - fastq_to_fasta_python + - fastq_dump + - regex1 + update_time: '2020-03-24' + versions: 2 +- create_time: '2020-03-22' + creators: [] + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 87ec5a48ebc848b5 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=87ec5a48ebc848b5 + name: Parallel accession download Illumina + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2020-03-23' + versions: 8 +- create_time: '2019-12-11' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Statistical calculation + - Formatting + - Sequence profile generation + - Format validation + - Sequence motif recognition + - Primer removal + - Coding region prediction + - Data retrieval + - Sequence assembly + - Sequencing quality control + - Protein feature detection + - Taxonomic classification + - Genome assembly + - Sequence composition calculation + - Database search + - Sequence trimming + - Gene prediction + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + - Read pre-processing + edam_topic: [] + id: 02631612a43a4d9b + latest_version: 27 + license: null + link: https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b + name: MetaG + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - sort1 + - __UNZIP_COLLECTION__ + - collapse_dataset + - fasplit + - tp_cat + - trim_galore + - hmmer_hmmscan + - tp_grep_tool + - tp_awk_tool + - __FLATTEN__ + - fraggenescan + - metaspades + - interproscan + - cat_bins + - maxbin2 + update_time: '2020-03-20' + versions: 27 +- create_time: '2020-02-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ac84daeb82d76e1c + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=ac84daeb82d76e1c + name: Center structures/trajectories + number_of_steps: null + source: https://usegalaxy.eu + tags: + - moleculardynamics + tools: + - gmx_trj + update_time: '2020-03-06' + versions: 3 +- create_time: '2020-02-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4516fe237a7112cc + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=4516fe237a7112cc + name: Peaks to Gene names & counts + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - Add_a_column1 + - gops_intersect_1 + - Grouping1 + - tp_replace_in_column + update_time: '2020-02-25' + versions: 0 +- create_time: '2018-08-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Primer removal + - Validation + - Variant calling + - Sequence trimming + - Sequence contamination filtering + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 6514e610c79df72c + latest_version: 13 + license: null + link: https://usegalaxy.eu/published/workflow?id=6514e610c79df72c + name: 3_CLIPseq-Explorer_demulti_Piranha_iCLIP_hg38 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CLIP-Explorer + tools: + - fastqc + - __UNZIP_COLLECTION__ + - deeptools_plot_fingerprint + - picard_CollectInsertSizeMetrics + - bctools_extract_alignment_ends + - piranha + - deeptools_compute_gc_bias + - bam_to_sam + - cat1 + - cutadapt + - rcas + - rna_star + - multiqc + - meme_chip + - __MERGE_COLLECTION__ + - Extract genomic DNA 1 + - ngsutils_bam_filter + - umi_tools_extract + - graphprot_predict_profile + - __SORTLIST__ + - tp_awk_tool + - bctools_extract_crosslinked_nucleotides + - bedtools_slopbed + - htseq_count + - samtools_flagstat + - umi_tools_dedup + - Filter1 + - bedtools_subtractbed + - bedtools_genomecoveragebed_bedgraph + - bedtools_sortbed + - deeptools_multi_bam_summary + - bedtools_intersectbed + - sam_to_bam + - wc_gnu + - bed2gff1 + - deeptools_plot_correlation + - Paste1 + - wig_to_bigWig + update_time: '2020-02-24' + versions: 13 +- create_time: '2018-08-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 153ba1581743d31f + latest_version: 18 + license: null + link: https://usegalaxy.eu/published/workflow?id=153ba1581743d31f + name: 1_CLIPseq-Explorer_demulti_PEAKachu_iCLIP_hg38 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CLIP-Explorer + tools: + - fastqc + - __UNZIP_COLLECTION__ + - peakachu + - deeptools_plot_fingerprint + - picard_CollectInsertSizeMetrics + - bctools_extract_alignment_ends + - deeptools_compute_gc_bias + - bam_to_sam + - cat1 + - cutadapt + - rcas + - rna_star + - multiqc + - meme_chip + - __MERGE_COLLECTION__ + - Extract genomic DNA 1 + - umi_tools_extract + - graphprot_predict_profile + - __SORTLIST__ + - tp_awk_tool + - bctools_extract_crosslinked_nucleotides + - bedtools_slopbed + - htseq_count + - samtools_flagstat + - umi_tools_dedup + - Filter1 + - bedtools_subtractbed + - bedtools_genomecoveragebed_bedgraph + - bedtools_sortbed + - deeptools_multi_bam_summary + - bedtools_intersectbed + - sam_to_bam + - wc_gnu + - Paste1 + - deeptools_plot_correlation + - wig_to_bigWig + update_time: '2020-02-24' + versions: 18 +- create_time: '2018-08-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Primer removal + - Validation + - Variant calling + - Sequence trimming + - Sequence contamination filtering + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 24ddd188da35b061 + latest_version: 17 + license: null + link: https://usegalaxy.eu/published/workflow?id=24ddd188da35b061 + name: 2_CLIPseq-Explorer_demulti_PureCLIP_iCLIP_hg38 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CLIP-Explorer + tools: + - fastqc + - deeptools_plot_fingerprint + - picard_CollectInsertSizeMetrics + - bctools_extract_alignment_ends + - deeptools_compute_gc_bias + - bam_to_sam + - cat1 + - cutadapt + - rcas + - rna_star + - multiqc + - meme_chip + - Extract genomic DNA 1 + - ngsutils_bam_filter + - umi_tools_extract + - graphprot_predict_profile + - tp_awk_tool + - bctools_extract_crosslinked_nucleotides + - bedtools_slopbed + - htseq_count + - samtools_flagstat + - umi_tools_dedup + - Filter1 + - bedtools_subtractbed + - bedtools_genomecoveragebed_bedgraph + - deeptools_multi_bam_summary + - bedtools_sortbed + - bedtools_intersectbed + - sam_to_bam + - deeptools_plot_correlation + - wc_gnu + - bed2gff1 + - Paste1 + - pureclip + - wig_to_bigWig + update_time: '2020-02-24' + versions: 17 +- create_time: '2018-08-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Primer removal + - Validation + - Variant calling + - Sequence trimming + - Sequence contamination filtering + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: b619339f4e1c6fdf + latest_version: 14 + license: null + link: https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf + name: 4_CLIPseq-Explorer_demulti_Piranha_eCLIP_hg38 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CLIP-Explorer + tools: + - fastqc + - __UNZIP_COLLECTION__ + - deeptools_plot_fingerprint + - picard_CollectInsertSizeMetrics + - bctools_extract_alignment_ends + - piranha + - deeptools_compute_gc_bias + - bam_to_sam + - cat1 + - cutadapt + - rcas + - rna_star + - multiqc + - meme_chip + - __MERGE_COLLECTION__ + - Extract genomic DNA 1 + - ngsutils_bam_filter + - umi_tools_extract + - graphprot_predict_profile + - __SORTLIST__ + - tp_awk_tool + - bctools_extract_crosslinked_nucleotides + - bedtools_slopbed + - htseq_count + - samtools_flagstat + - umi_tools_dedup + - Filter1 + - bedtools_subtractbed + - bedtools_genomecoveragebed_bedgraph + - bedtools_sortbed + - deeptools_multi_bam_summary + - bedtools_intersectbed + - sam_to_bam + - wc_gnu + - bed2gff1 + - deeptools_plot_correlation + - Paste1 + - wig_to_bigWig + update_time: '2020-02-24' + versions: 14 +- create_time: '2018-08-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Primer removal + - Validation + - Variant calling + - Sequence trimming + - Sequence contamination filtering + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 8fb156020285e049 + latest_version: 22 + license: null + link: https://usegalaxy.eu/published/workflow?id=8fb156020285e049 + name: 3_CLIPseq-Explorer_demulti_PureCLIP_eCLIP_hg38 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CLIP-Explorer + tools: + - fastqc + - deeptools_plot_fingerprint + - picard_CollectInsertSizeMetrics + - bctools_extract_alignment_ends + - deeptools_compute_gc_bias + - bam_to_sam + - cat1 + - cutadapt + - rcas + - rna_star + - multiqc + - meme_chip + - Extract genomic DNA 1 + - ngsutils_bam_filter + - umi_tools_extract + - graphprot_predict_profile + - tp_awk_tool + - bctools_extract_crosslinked_nucleotides + - bedtools_slopbed + - htseq_count + - samtools_flagstat + - umi_tools_dedup + - Filter1 + - bedtools_subtractbed + - bedtools_genomecoveragebed_bedgraph + - deeptools_multi_bam_summary + - bedtools_sortbed + - bedtools_intersectbed + - sam_to_bam + - deeptools_plot_correlation + - wc_gnu + - bed2gff1 + - Paste1 + - pureclip + - wig_to_bigWig + update_time: '2020-02-24' + versions: 22 +- create_time: '2018-08-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 0c619b25c1394a09 + latest_version: 15 + license: null + link: https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09 + name: 2_CLIPseq-Explorer_demulti_PEAKachu_eCLIP_hg38 + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CLIP-Explorer + tools: + - fastqc + - __UNZIP_COLLECTION__ + - peakachu + - deeptools_plot_fingerprint + - picard_CollectInsertSizeMetrics + - bctools_extract_alignment_ends + - deeptools_compute_gc_bias + - bam_to_sam + - cat1 + - cutadapt + - rcas + - rna_star + - multiqc + - meme_chip + - __MERGE_COLLECTION__ + - Extract genomic DNA 1 + - umi_tools_extract + - graphprot_predict_profile + - __SORTLIST__ + - tp_awk_tool + - bctools_extract_crosslinked_nucleotides + - bedtools_slopbed + - htseq_count + - samtools_flagstat + - umi_tools_dedup + - Filter1 + - bedtools_subtractbed + - bedtools_genomecoveragebed_bedgraph + - bedtools_sortbed + - deeptools_multi_bam_summary + - bedtools_intersectbed + - sam_to_bam + - wc_gnu + - Paste1 + - deeptools_plot_correlation + - wig_to_bigWig + update_time: '2020-02-24' + versions: 15 +- create_time: '2020-02-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Generation + - Sequencing quality control + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: dd3193aaaf08e798 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=dd3193aaaf08e798 + name: 'COVID-19: read pre-processing without downloading from SRA' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - picard_MergeSamFiles + - minimap2 + - multiqc + - samtool_filter2 + - bwa_mem + update_time: '2020-02-23' + versions: 1 +- create_time: '2020-02-21' + creators: [] + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: 402b14906a03b2ef + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=402b14906a03b2ef + name: 'COVID-19: CoV S-gene conservation' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + tools: + - 'EMBOSS: tranalign100' + - 'EMBOSS: transeq101' + - rbc_mafft + update_time: '2020-02-21' + versions: 2 +- create_time: '2020-02-21' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Statistical calculation + - Sequence alignment analysis + - Local alignment + - Phylogenetic tree generation (from molecular sequences) + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: e7f03b4bd9b3d6fd + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd + name: 'COVID-19: Recombination and selection analysis' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + tools: + - hyphy_gard + - rbc_mafft + - 'EMBOSS: tranalign100' + - hyphy_absrel + - fasttree + - 'EMBOSS: transeq101' + update_time: '2020-02-21' + versions: 2 +- create_time: '2020-02-21' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + - Formatting + - Phylogenetic tree generation (from molecular sequences) + edam_topic: [] + id: 9155ed0e7a6a7b60 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60 + name: 'COVID-19: MRCA analysis' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + tools: + - picard_NormalizeFasta + - Remove beginning1 + - Cut1 + - collapse_dataset + - ncbi_acc_download + - rbc_mafft + - fasttree + - tp_sed_tool + - Convert characters1 + update_time: '2020-02-21' + versions: 2 +- create_time: '2020-02-20' + creators: [] + doi: '' + edam_operation: + - Sequence assembly visualisation + - Aggregation + - Genome assembly + edam_topic: [] + id: 7b755497d168cb13 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=7b755497d168cb13 + name: 'COVID-19: assembly of genome sequence' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - COVID-19 + tools: + - bandage_image + - spades + - unicycler + - bandage_info + update_time: '2020-02-21' + versions: 2 +- create_time: '2020-02-19' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + edam_topic: [] + id: 3e0246389fb70340 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3e0246389fb70340 + name: Workflow constructed from history 'Galaxy training session Tours 11th February + 2020 - Barcoding' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_tail_tool + - tab2fasta + - clustalw + - ncbi_blastn_wrapper + - ncbi_makeblastdb + update_time: '2020-02-19' + versions: 0 +- create_time: '2020-02-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e73beff62f35d677 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e73beff62f35d677 + name: 'imported: Hsp90-ligand workflow' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - get_pdb + - ambertools_acpype + - gmx_sim + - gmx_editconf + - gmx_em + - gmx_setup + - tp_grep_tool + - gmx_solvate + - gmx_restraints + - gmx_makendx + - openbabel_compound_convert + update_time: '2020-02-14' + versions: 1 +- create_time: '2020-01-06' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Read mapping + - Nucleic acid sequence analysis + edam_topic: [] + id: 5b46c8533cd95447 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=5b46c8533cd95447 + name: RNAseq_UMG_SDumont_v1 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - htseq_count + - bowtie2 + - deseq2 + - Filter1 + update_time: '2020-02-13' + versions: 2 +- create_time: '2020-01-31' + creators: [] + doi: '' + edam_operation: + - De-novo assembly + - Coding region prediction + - Pairwise sequence alignment + - Genome annotation + - Antimicrobial resistance prediction + - Box-Whisker plot plotting + - Filtering + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + - Genome visualisation + - Taxonomic classification + - Genome assembly + - Visualisation + - Scatter plot plotting + - Cross-assembly + - Mapping assembly + - Gene prediction + - Multilocus sequence typing + edam_topic: [] + id: a337bfb2eb1e583f + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f + name: MetaGalaxy (4x polishing w Racon) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Nanopore + - Metagenomics + - ONT + tools: + - nanoplot + - abricate + - taxonomy_krona_chart + - quast + - Cut1 + - flye + - bandage_info + - racon + - filtlong + - prokka + - kraken2 + - mlst + - jbrowse + - minimap2 + - bandage_image + update_time: '2020-02-10' + versions: 4 +- create_time: '2020-01-24' + creators: [] + doi: '' + edam_operation: + - De-novo assembly + - Coding region prediction + - Pairwise sequence alignment + - Genome annotation + - Antimicrobial resistance prediction + - Box-Whisker plot plotting + - Filtering + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + - Genome visualisation + - Taxonomic classification + - Genome assembly + - Visualisation + - Scatter plot plotting + - Cross-assembly + - Mapping assembly + - Gene prediction + - Multilocus sequence typing + edam_topic: [] + id: a84bac86ec183d46 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46 + name: MetaGalaxy + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Nanopore + - Metagenomics + - ONT + tools: + - nanoplot + - abricate + - taxonomy_krona_chart + - quast + - Cut1 + - flye + - bandage_info + - racon + - filtlong + - prokka + - kraken2 + - mlst + - jbrowse + - minimap2 + - bandage_image + update_time: '2020-02-10' + versions: 8 +- create_time: '2020-01-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a824fb7e65a1a939 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=a824fb7e65a1a939 + name: Regression (from training material) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ml + tools: + - Remove beginning1 + - sklearn_build_pipeline + - sklearn_ensemble + - plotly_regression_performance_plots + - sklearn_generalized_linear + - sklearn_searchcv + update_time: '2020-01-24' + versions: 2 +- create_time: '2020-01-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3e91f8417a66d02c + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=3e91f8417a66d02c + name: Find exons with the highest number of interactions + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2020-01-22' + versions: 3 +- create_time: '2020-01-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b711696909ee2b59 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=b711696909ee2b59 + name: FindExons with the highest number of interactions + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2020-01-15' + versions: 2 +- create_time: '2020-01-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 81abf01f79f358fe + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=81abf01f79f358fe + name: Find exons with the highest numbers of interactions + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2020-01-15' + versions: 1 +- create_time: '2020-01-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7fbde7faec75c781 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=7fbde7faec75c781 + name: 'Workflow ''tutorial101'': find exons with the highest number of SNPs' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2020-01-15' + versions: 4 +- create_time: '2019-11-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d873ff816f028d4f + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=d873ff816f028d4f + name: T4L dcTMD + number_of_steps: null + source: https://usegalaxy.eu + tags: + - moleculardynamics + tools: + - gmx_sim + update_time: '2020-01-11' + versions: 5 +- create_time: '2020-01-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a669986e1a5cee31 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a669986e1a5cee31 + name: Age prediction from DNA methylation (from training material) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ml + tools: + - plotly_regression_performance_plots + - sklearn_build_pipeline + - sklearn_searchcv + - sklearn_ensemble + update_time: '2020-01-10' + versions: 1 +- create_time: '2020-01-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 83fe480cdbb70099 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=83fe480cdbb70099 + name: Age prediction from RNASeq (from training material) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ml + tools: + - sklearn_build_pipeline + - plotly_parallel_coordinates_plot + - sklearn_searchcv + update_time: '2020-01-10' + versions: 1 +- create_time: '2020-01-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 17e99647745eb150 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=17e99647745eb150 + name: Basics of machine learning (from training material) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ml + tools: + - sklearn_svm_classifier + update_time: '2020-01-09' + versions: 2 +- create_time: '2020-01-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fdbf1a1a584a429c + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=fdbf1a1a584a429c + name: Machine learning - classification (from training material) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ml + tools: + - plotly_ml_performance_plots + - sklearn_svm_classifier + update_time: '2020-01-09' + versions: 2 +- create_time: '2020-01-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4b383d13ff512687 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=4b383d13ff512687 + name: Machine learning - regression (from training material) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ml + tools: + - plotly_regression_performance_plots + - sklearn_ensemble + update_time: '2020-01-09' + versions: 2 +- create_time: '2019-07-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 50f8693fac7e134b + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=50f8693fac7e134b + name: EBI Single Cell Expression Atlas Scanpy Prod 1.3 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_find_variable_genes + - scanpy_find_cluster + - scanpy_read_10x + - scanpy_compute_graph + - scanpy_find_markers + - _ensembl_gtf2gene_list + - scanpy_normalise_data + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_parameter_iterator + - scanpy_run_pca + update_time: '2020-01-09' + versions: 4 +- create_time: '2019-10-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5d31bafd82547d5d + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d + name: Atlas-Seurat-CellBrowser + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - seurat_filter_cells + - seurat_find_variable_genes + - seurat_run_pca + - seurat_export_cellbrowser + - ucsc_cell_browser + - seurat_read10x + - seurat_find_clusters + - seurat_scale_data + - seurat_dim_plot + - seurat_find_markers + - seurat_create_seurat_object + - seurat_run_tsne + - seurat_normalise_data + - retrieve_scxa + update_time: '2020-01-09' + versions: 2 +- create_time: '2020-01-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b351b297ac7d923f + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=b351b297ac7d923f + name: Hole filling + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + tools: + - ctb_chemfp_mol2fps + - Remove beginning1 + - tp_cat + - tp_grep_tool + - tp_cut_tool + - ctb_simsearch + - comp1 + - ctb_chemfp_butina_clustering + - Show beginning1 + update_time: '2020-01-09' + versions: 5 +- create_time: '2020-01-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 77fa6e5a8fa3f911 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=77fa6e5a8fa3f911 + name: Cheminformatics-ML + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + - ml + tools: + - openbabel_remDuplicates + - Remove beginning1 + - Cut1 + - sklearn_ensemble + - tp_grep_tool + - tp_replace_in_column + - tp_easyjoin_tool + - ctb_mordred_descriptors + - tp_sorted_uniq + - plotly_ml_performance_plots + - Paste1 + - sklearn_train_test_split + - openbabel_remIons + update_time: '2020-01-09' + versions: 5 +- create_time: '2019-12-23' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: 41268469c6616e42 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=41268469c6616e42 + name: Workflow constructed from history 'JBrowse Tutorial (again)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - jbrowse + update_time: '2019-12-23' + versions: 1 +- create_time: '2019-12-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f7a7c72489d6b3d4 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4 + name: Compound library download + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + tools: + - openbabel_remIons + - Cut1 + - bg_uniq + - mergeCols1 + - tp_grep_tool + - cat1 + - Grep1 + - Convert characters1 + - ctb_pubchem_download_as_smiles + - sed_stream_editor + - addValue + - ctb_online_data_fetch + - openbabel_compound_convert + - Filter1 + update_time: '2019-12-20' + versions: 3 +- create_time: '2019-12-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 16ab4c91858942dd + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=16ab4c91858942dd + name: Protein-ligand docking + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + tools: + - chembl + - get_pdb + - prepare_box + - tp_grep_tool + - sdf_to_tab + - prepare_receptor + - docking + - openbabel_compound_convert + update_time: '2019-12-20' + versions: 2 +- create_time: '2019-12-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b4642b1e0985f76b + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=b4642b1e0985f76b + name: Cheminformatics training material + number_of_steps: null + source: https://usegalaxy.eu + tags: + - cheminformatics + tools: + - chembl + - ctb_chemfp_mol2fps + - get_pdb + - collapse_dataset + - tp_cat + - prepare_box + - tp_grep_tool + - sdf_to_tab + - prepare_receptor + - docking + - addValue + - ctb_chemfp_nxn_clustering + - ctb_chemfp_butina_clustering + - openbabel_compound_convert + update_time: '2019-12-20' + versions: 2 +- create_time: '2019-12-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 08bbf87ab2a2230e + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=08bbf87ab2a2230e + name: Workflow3_Novel_peptide_analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Proteogenomics + tools: + - query_tabular + - peptide_genomic_coordinate + - pep_pointer + update_time: '2019-12-17' + versions: 3 +- create_time: '2019-12-05' + creators: [] + doi: '' + edam_operation: + - Peptide database search + - Conversion + edam_topic: [] + id: edea08c943ff9c5e + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e + name: Workflow2_RNAseq_DBsearch + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Proteogenomics + tools: + - ncbi_blastp_wrapper + - Cut1 + - query_tabular + - fasta2tab + - mz_to_sqlite + - Grouping1 + - Convert characters1 + - tab2fasta + - peptide_shaker + - search_gui + update_time: '2019-12-17' + versions: 6 +- create_time: '2019-03-25' + creators: [] + doi: '' + edam_operation: + - Variant calling + - RNA-Seq analysis + - Transcriptome assembly + - Statistical calculation + - Sequence alignment + - Sequence annotation + edam_topic: [] + id: a2f36d4dd48d8ec2 + latest_version: 17 + license: null + link: https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2 + name: Workflow1_RNAseq_DBcreation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Proteogenomics + tools: + - tp_replace_in_line + - tp_cat + - stringtie + - query_tabular + - regexColumn1 + - fasta_merge_files_and_filter_unique_sequences + - bed_to_protein_map + - tp_replace_in_column + - hisat2 + - gffcompare + - gffcompare_to_bed + - custom_pro_db + - sqlite_to_tabular + - translate_bed + - freebayes + update_time: '2019-12-17' + versions: 17 +- create_time: '2019-12-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Coding region prediction + - Validation + - Genome annotation + - Antimicrobial resistance prediction + - Gene prediction + - Sequencing quality control + - Multilocus sequence typing + edam_topic: [] + id: 42c0da2e86318b37 + latest_version: 15 + license: null + link: https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37 + name: Bacterial_WGS_Tutorial + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - abricate + - trimmomatic + - shovill + - mlst + - prokka + - __FLATTEN__ + - multiqc + update_time: '2019-12-12' + versions: 15 +- create_time: '2019-04-15' + creators: [] + doi: '' + edam_operation: + - Validation + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - Sequence composition calculation + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 0fa523529c4f73cf + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=0fa523529c4f73cf + name: STAR_Globin-Block + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - htseq_count + - rna_star + - multiqc + - deseq2 + update_time: '2019-12-10' + versions: 2 +- create_time: '2019-12-03' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: d7c0c972c471d514 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=d7c0c972c471d514 + name: Explore filtering v0.2.8 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - scanpy_filter_genes + - scanpy_plot + - scanpy_filter_cells + update_time: '2019-12-03' + versions: 2 +- create_time: '2019-12-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Genome indexing + - Sequence composition calculation + - Read mapping + - Read summarisation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b86f3775aa1f13bc + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=b86f3775aa1f13bc + name: 'Workflow constructed from history ''imported: Genomics 2019 TnSeq data''' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - Cut1 + - tp_sort_header_tool + - Add_a_column1 + - fasterq_dump + - bwa + - fastq_dump + - tp_easyjoin_tool + - bg_find_subsequences + - deeptools_bam_coverage + - featurecounts + update_time: '2019-12-02' + versions: 0 +- create_time: '2019-11-25' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 921cab3e6faf30be + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=921cab3e6faf30be + name: 'Scanpy: Clustering 3K PBMCs' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - anndata_manipulate + - scanpy_filter + - anndata_inspect + - Cut1 + - tp_cat + - scanpy_cluster_reduce_dimension + - scanpy_normalize + - tp_replace_in_column + - tp_tail_tool + - tp_awk_tool + - scanpy_plot + - scanpy_remove_confounders + - anndata_import + - scanpy_inspect + update_time: '2019-11-25' + versions: 1 +- create_time: '2019-11-01' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Operation + - Genome assembly + - Sequence annotation + - Homology-based gene prediction + - Scaffolding + - Genome annotation + - Transcriptome assembly + - Sequence assembly validation + - Gene prediction + - Ab-initio gene prediction + edam_topic: [] + id: 6ca20e710f4f3ffb + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb + name: Workflow constructed from history 'Homework 6' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snap_training + - gffread + - jcvi_gff_stats + - fasta-stats + - jbrowse + - 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October + 2019_newparams_18 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - search_gui + - peptide_shaker + update_time: '2019-10-28' + versions: 6 +- create_time: '2019-10-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 249c7569b61fb349 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=249c7569b61fb349 + name: SearchGUI Peptide Shaker Workflow for SIHUMI - October 2019_newparams_5 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - search_gui + - peptide_shaker + update_time: '2019-10-28' + versions: 4 +- create_time: '2019-10-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7dd7908f4c8d722a + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a + name: SectioningWorkflow_GalaxyP + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - split_file_to_collection + - filter_by_fasta_ids + - tp_sort_header_tool + - Cut1 + - query_tabular + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - tp_easyjoin_tool + - peptide_shaker + - addValue + - dbbuilder + - search_gui + update_time: '2019-10-24' + versions: 2 +- create_time: '2019-02-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d2a9d4eb5b3c72a2 + latest_version: 18 + license: null + link: https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2 + name: SectioningWorkflow_GalaxyP + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - split_file_to_collection + - filter_by_fasta_ids + - tp_sort_header_tool + - Cut1 + - query_tabular + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - tp_easyjoin_tool + - peptide_shaker + - addValue + - dbbuilder + - search_gui + update_time: '2019-10-24' + versions: 18 +- create_time: '2019-10-23' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Genome assembly + - Sequence assembly visualisation + - Filtering + - Read pre-processing + - Primer removal + - Aggregation + - Sequencing quality control + edam_topic: [] + id: 346b46e6316c6950 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=346b46e6316c6950 + name: ONT -- Unicycler + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ONT + tools: + - unicycler + - trim_galore + - filtlong + - porechop + - bandage_image + update_time: '2019-10-23' + versions: 1 +- create_time: '2019-10-22' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Genome assembly + - Mapping assembly + - De-novo assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: 32d2f5340098bcbd + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd + name: ONT -- Long-Read-Assembly + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ONT + tools: + - nanoplot + - staramr_search + - PlasFlow + - racon + - gfa_to_fa + - miniasm + - minimap2 + - bandage_image + update_time: '2019-10-22' + versions: 1 +- create_time: '2019-10-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Generation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 11290f22e13899bd + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=11290f22e13899bd + name: Workflow constructed from history 'Homework 4' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - bam_to_sam + - bwa + - deeptools_bam_coverage + - bowtie2 + update_time: '2019-10-18' + versions: 0 +- create_time: '2019-10-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - 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tp_cat + - bedtools_intersectbed + - Filter1 + update_time: '2019-10-18' + versions: 0 +- create_time: '2019-10-14' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: 8048cadfd1ed1661 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=8048cadfd1ed1661 + name: Workflow constructed from history 'ecoli prep' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - jbrowse + update_time: '2019-10-14' + versions: 0 +- create_time: '2019-10-07' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - RNA-Seq quantification + - Sequence alignment + - Read summarisation + - Sequence annotation + edam_topic: [] + id: 2287afbf248d9c89 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=2287afbf248d9c89 + name: Workflow constructed from history 'week 7 one last time' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - trimmomatic + - stringtie + - Grep1 + - gffcompare + - deeptools_bam_coverage + - Filter1 + - stringtie_merge + - featurecounts + - deseq2 + - hisat2 + update_time: '2019-10-07' + versions: 0 +- create_time: '2019-10-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Generation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: da5d4e3e6c66cf3b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=da5d4e3e6c66cf3b + name: Workflow constructed from history 'Homework 4' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - bam_to_sam + - bwa + - deeptools_bam_coverage + - bowtie2 + update_time: '2019-10-04' + versions: 0 +- create_time: '2019-09-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f34c76e2d8045725 + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=f34c76e2d8045725 + name: SearchGUI Peptide Shaker Workflow for SIHUMI - September 2019 + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - search_gui + - peptide_shaker + update_time: '2019-09-30' + versions: 11 +- create_time: '2019-09-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome assembly + - De-novo assembly + - Sequence composition calculation + - Aggregation + - Visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 842e0ea7b1eb56af + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af + name: Workflow constructed from history 'homework 3' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - velvetg + - quast + - unicycler + - fastq_paired_end_interlacer + - velveth + update_time: '2019-09-27' + versions: 0 +- create_time: '2019-09-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 68edbb8eec38ad00 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=68edbb8eec38ad00 + name: N-TAILS workflow for IPS + number_of_steps: null + source: https://usegalaxy.eu + tags: + - IPS + tools: + - HighResPrecursorMassCorrector + - FalseDiscoveryRate + - IDConflictResolver + - IDFilter + - MultiplexResolver + - IDMerger + - FeatureFinderMultiplex + - ConsensusID + - MSGFPlusAdapter + - IDMapper + - FileFilter + - MzTabExporter + - PeptideIndexer + - FileMerger + update_time: '2019-09-25' + versions: 4 +- create_time: '2019-09-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 805979703dc7cc01 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=805979703dc7cc01 + name: Merge Batches + number_of_steps: null + source: https://usegalaxy.eu + tags: + - peters + - meinbio + tools: + - tp_sed_tool + - table_compute + - tp_awk_tool + update_time: '2019-09-23' + versions: 1 +- create_time: '2019-07-04' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 8e92a65d3307d87e + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=8e92a65d3307d87e + name: Regional GAM workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Count1 + - regionalgam_glmmpql + - regionalgam_gls + - regionalgam_flight_curve + - regionalgam_ab_index + - regionalgam_plot_trend + - tp_awk_tool + - ggplot2_point + - regionalgam_autocor_acf + update_time: '2019-09-23' + versions: 2 +- create_time: '2019-09-21' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Sequence analysis + - Statistical calculation + - Genetic variation analysis + edam_topic: [] + id: 3570835f21365be7 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=3570835f21365be7 + name: exome_seq_training_short_w_cached_ref + number_of_steps: null + source: https://usegalaxy.eu + tags: + - variant-analysis + - training-material + tools: + - gemini_inheritance + - gemini_load + - samtools_rmdup + - bcftools_norm + - snpEff + - samtool_filter2 + - freebayes + update_time: '2019-09-21' + versions: 1 +- create_time: '2019-09-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Variant calling + - Sequence analysis + - Generation + - Sequence alignment + - Genetic variation analysis + - Sequencing quality control + edam_topic: [] + id: 2aede5c6577b28f5 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=2aede5c6577b28f5 + name: exome_seq_training_full_w_cached_ref + number_of_steps: null + source: https://usegalaxy.eu + tags: + - variant-analysis + - training-material + tools: + - fastqc + - gemini_inheritance + - gemini_load + - samtools_rmdup + - bcftools_norm + - snpEff + - multiqc + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2019-09-21' + versions: 1 +- create_time: '2019-09-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c15303fcc0b53df6 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=c15303fcc0b53df6 + name: Age Prediction and Seek workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sklearn_build_pipeline + - plotly_parallel_coordinates_plot + - sklearn_searchcv + - sklearn_estimator_attributes + update_time: '2019-09-16' + versions: 1 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: + - Validation + - Read summarisation + - Data handling + - Sequence alignment analysis + - RNA-Seq quantification + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 49073a24429d93d6 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=49073a24429d93d6 + name: 'CelSeq2: Single Batch mm10' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - umi_tools_extract + - bamFilter + - umi_tools_count + - tp_sed_tool + - samtools_stats + - rna_star + - multiqc + - featurecounts + update_time: '2019-09-04' + versions: 5 +- create_time: '2019-08-30' + creators: [] + doi: '' + edam_operation: + - Community profiling + - Sequence alignment + - Loading + edam_topic: [] + id: a1cfb476e849fce3 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=a1cfb476e849fce3 + name: 10X StarSolo Workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rna_starsolo + - dropletutils + update_time: '2019-08-30' + versions: 2 +- create_time: '2019-01-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6d7d354948e8dee1 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=6d7d354948e8dee1 + name: Email me + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - secure_hash_message_digest + update_time: '2019-08-09' + versions: 2 +- create_time: '2019-08-07' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Primer removal + - Sequence trimming + - Visualisation + - Sequence clustering + - DNA barcoding + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b91a380ceaa0342b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=b91a380ceaa0342b + name: 16s_mothur_schisto + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mothur_align_seqs + - mothur_classify_seqs + - taxonomy_krona_chart + - trim_galore + - mothur_make_shared + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_unique_seqs + - mothur_taxonomy_to_krona + - mothur_classify_otu + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - mothur_count_groups + - mothur_cluster_split + - mothur_make_biom + - mothur_pre_cluster + update_time: '2019-08-07' + versions: 0 +- create_time: '2019-08-05' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Primer removal + - Sequence trimming + - Visualisation + - Sequence clustering + - DNA barcoding + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b66e1d8171e6dac2 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=b66e1d8171e6dac2 + name: 16s_mothur_schisto + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mothur_align_seqs + - mothur_classify_seqs + - taxonomy_krona_chart + - trim_galore + - mothur_make_shared + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_unique_seqs + - mothur_taxonomy_to_krona + - mothur_classify_otu + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - mothur_count_groups + - mothur_cluster_split + - mothur_make_biom + - mothur_pre_cluster + update_time: '2019-08-05' + versions: 2 +- create_time: '2019-07-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c0888e0a0fb53ed3 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=c0888e0a0fb53ed3 + name: Bilan enrichi Point Fixe + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - vigiechiro_idcorrect_2ndlayer + - vigiechiro_idvalid + - vigiechiro_bilanenrichipf + update_time: '2019-07-31' + versions: 2 +- create_time: '2019-07-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 596b073ab7249aa2 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=596b073ab7249aa2 + name: "Bilan enrichi Routier ou P\xE9destre" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - 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Training + - GCC2019 + tools: + - IDConflictResolver + - MultiplexResolver + - FileFilter + update_time: '2019-06-06' + versions: 1 +- create_time: '2019-05-25' + creators: [] + doi: '' + edam_operation: + - Annotation + edam_topic: [] + id: 36eefcc25ab1fe15 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=36eefcc25ab1fe15 + name: refid2name + number_of_steps: null + source: https://usegalaxy.eu + tags: + - id2name + tools: + - annotatemyids + - tp_find_and_replace + update_time: '2019-05-25' + versions: 2 +- create_time: '2019-05-21' + creators: [] + doi: '' + edam_operation: + - Validation + - Read summarisation + - Data handling + - Sequence alignment analysis + - RNA-Seq quantification + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f841e1207611f28f + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=f841e1207611f28f + name: ymjbb + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - 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name:ONT + - ONT + tools: + - nanopolish_variants + - flye + - racon + - bam_to_sam + - filtlong + - minimap2 + update_time: '2019-05-22' + versions: 2 +- create_time: '2019-05-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 71a3534a6dc573ed + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=71a3534a6dc573ed + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - datamash_ops + - join1 + update_time: '2019-05-13' + versions: 1 +- create_time: '2019-05-03' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + - Mapping + edam_topic: [] + id: a06b1ed5cd25922f + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f + name: "Patricija, Salom\u0117ja, Airidas" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - staramr_search + - bedtools_randombed + - rbc_mafft + update_time: '2019-05-03' + versions: 0 +- create_time: '2019-05-03' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + edam_topic: [] + id: 941400d10c346b2c + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=941400d10c346b2c + name: MAFFT workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rbc_mafft + update_time: '2019-05-03' + versions: 0 +- create_time: '2019-04-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b47e415f80941ba0 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=b47e415f80941ba0 + name: Analysis using MDAnalysis + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mdanalysis_rdf + - mdanalysis_ramachandran_plot + - mdanalysis_cosine_analysis + - mdanalysis_dihedral + - mdanalysis_distance + update_time: '2019-04-30' + versions: 0 +- create_time: '2019-03-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a5ca8b9807ed3f73 + latest_version: 23 + license: null + link: https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73 + name: MSI of N-linked glycans re-analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - 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massspectrometryimaging + tools: + - tp_replace_in_line + - Remove beginning1 + - Cut1 + - tp_split_on_column + update_time: '2019-04-11' + versions: 14 +- create_time: '2019-01-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1f3f6757de60d3cf + latest_version: 14 + license: null + link: https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf + name: Bruker ROI.xml conversion to annotation tabular file + number_of_steps: null + source: https://usegalaxy.eu + tags: + - massspectrometryimaging + tools: + - xpath + - Cut1 + - addName + - tp_replace_in_line + - tp_cat + - __RELABEL_FROM_FILE__ + - tp_split_on_column + update_time: '2019-04-11' + versions: 14 +- create_time: '2018-11-13' + creators: [] + doi: '' + edam_operation: + - Variant calling + - RNA-Seq analysis + - Transcriptome assembly + - Statistical calculation + - Sequence alignment + - Sequence annotation + edam_topic: [] + id: 6e6cf59bfeb938bf + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf + name: MousePG_Workflow1_RNAseq_DBcreation (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_replace_in_line + - tp_cat + - query_tabular + - stringtie + - fasta_merge_files_and_filter_unique_sequences + - bed_to_protein_map + - tp_replace_in_column + - hisat2 + - gffcompare + - gffcompare_to_bed + - custom_pro_db + - sqlite_to_tabular + - translate_bed + - freebayes + update_time: '2019-03-29' + versions: 2 +- create_time: '2019-03-16' + creators: [] + doi: '' + edam_operation: + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - RNA-Seq quantification + - Sequence alignment + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 17ad465d9515cd25 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25 + name: "Workflow analyse differentielle lign\xE9es cellulaire souris-LW" + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - tp_sort_header_tool + - Add_a_column1 + - tp_cat + - stringtie + - XY_Plot_1 + - ggplot2_heatmap2 + - tp_easyjoin_tool + - scatterplot_rpy + - volcanoplot + - multiqc + - Filter1 + - tp_multijoin_tool + - featurecounts + - deseq2 + - hisat2 + update_time: '2019-03-16' + versions: 4 +- create_time: '2019-03-01' + creators: [] + doi: '' + edam_operation: + - Formatting + - Visualisation + - Prediction and recognition + - Filtering + - Label-free quantification + edam_topic: [] + id: ba3a5d59b3879764 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764 + name: imetaQuantome_datacreation_workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - regex_replace + - query_tabular + - tp_replace_in_column + - flashlfq + - peptide_shaker + - search_gui + - unipept + - msconvert + - Filter1 + update_time: '2019-03-01' + versions: 4 +- create_time: '2019-02-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence alignment analysis + - Phylogenetic inference + - Primer removal + - Sequencing quality control + - Taxonomic classification + - Sequence composition calculation + - Sequence comparison + - Phylogenetic tree visualisation + - Sequence trimming + - Visualisation + - Conversion + - Read pre-processing + - Sequence similarity search + - Phylogenetic tree editing + edam_topic: [] + id: 2cf09adb1ed6c3ec + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec + name: 2/22 Pilot ASAIM + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - metaphlan2krona + - format_metaphlan2_output + - group_humann2_uniref_abundances_to_go + - taxonomy_krona_chart + - export2graphlan + - regex_replace + - trim_galore + - fastq_paired_end_joiner + - humann2_genefamilies_genus_level + - metaphlan2 + - humann2 + - graphlan + - bg_sortmerna + - fastq_groomer + - combine_metaphlan2_humann2 + - graphlan_annotate + update_time: '2019-02-22' + versions: 3 +- create_time: '2019-01-28' + creators: [] + doi: '' + edam_operation: + - 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infernal_cmbuild + - preMloc + - locarna_best_subtree + - infernal_cmsearch + - structure_to_gspan + update_time: '2019-02-03' + versions: 2 +- create_time: '2019-01-28' + creators: [] + doi: '' + edam_operation: + - Nucleic acid feature detection + edam_topic: [] + id: 9b1b135109072e71 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=9b1b135109072e71 + name: GraphClust_main_1r + number_of_steps: null + source: https://usegalaxy.eu + tags: + - PUBLISHED + tools: + - cmFinder + - NSPDK_candidateClust + - preproc + - viennarna_rnafold + - nspdk_sparse + - glob_report + - infernal_cmbuild + - preMloc + - locarna_best_subtree + - infernal_cmsearch + - structure_to_gspan + update_time: '2019-02-03' + versions: 2 +- create_time: '2019-02-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Sequence annotation + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 0de150b19102cb7e + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=0de150b19102cb7e + name: 'Updated tool versions: De novo transcriptome reconstruction with RNA-Seq' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trimmomatic + - stringtie + - gffcompare + - deeptools_bam_coverage + - Filter1 + - stringtie_merge + - featurecounts + - deseq2 + - hisat2 + update_time: '2019-02-01' + versions: 3 +- create_time: '2019-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 58fd339165ded462 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=58fd339165ded462 + name: ViennaRNA_Introduction + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - viennarna_rnafold + - viennarna_rnaplot + - viennarna_rnaalifold + update_time: '2019-02-01' + versions: 0 +- create_time: '2019-01-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: bab0322cc0346d81 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=bab0322cc0346d81 + name: 'imported: ASaiM - Shotgun workflow for paired-end data' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastq_paired_end_joiner + update_time: '2019-01-30' + versions: 1 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 17e720bee3b9104f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=17e720bee3b9104f + name: Visualization of RNA-Seq results with CummeRbund + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - RNA-seq + - visualization + tools: + - cummerbund_to_cuffdiff + - cummeRbund + - tp_sort_header_tool + - Filter1 + update_time: '2019-01-25' + versions: 1 +- create_time: '2019-01-23' + creators: [] + doi: '' + edam_operation: + - Nucleic acid feature detection + edam_topic: [] + id: 8f2d958cee428ca1 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1 + name: RNA family model construction + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - Family + - Model + tools: + - RNAlien + - selectsequencesfrommsa + - rbc_rnacode + - cmv + - rnaz + - infernal_cmstat + update_time: '2019-01-23' + versions: 0 +- create_time: '2019-01-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3b717623054d5125 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3b717623054d5125 + name: scan for C/D-box sequences with segmentation-fold + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - C/D-box + - snoRNA + tools: + - smf_utils_fix-fasta-headers + - smf_utils_extract-boxed-sequences + - smf_utils_filter-by-energy + - smf_utils_find-boxes + - smf_utils_estimate-energy + update_time: '2019-01-23' + versions: 0 +- create_time: '2019-01-23' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 4e57c5cf750afadd + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=4e57c5cf750afadd + name: AREsite2_CLIP_analysis (imported from API) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - CLIP-seq + tools: + - sort1 + - Cut1 + - cat1 + - bedtools_intersectbed + - addValue + - AREsite2_REST + update_time: '2019-01-23' + versions: 0 +- create_time: '2019-01-23' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + - Nucleic acid feature detection + edam_topic: [] + id: 5cd167ed9e159e73 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73 + name: Analyse unaligned ncRNAs + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - Alignment + - MSA + - Folding + - Structure + - Sequence + tools: + - rbc_rnacode + - selectsequencesfrommsa + - viennarna_rnaalifold + - cmv + - rbc_mafft + - rnaz + - locarna_multiple + - infernal_cmbuild + - infernal_cmsearch + - infernal_cmstat + update_time: '2019-01-23' + versions: 0 +- create_time: '2019-01-23' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Read mapping + - Primer removal + - Read pre-processing + edam_topic: [] + id: a108b575b16e6cb9 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a108b575b16e6cb9 + name: PAR-CLIP analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - PAR-CLIP + tools: + - paralyzer + - bowtie2 + - trim_galore + update_time: '2019-01-23' + versions: 1 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Pathway or network analysis + edam_topic: [] + id: 12c80c5b5e2305d8 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=12c80c5b5e2305d8 + name: Network analysis with Heinz + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - metatranscriptomics + - network + - pathway + tools: + - heinz_bum + - heinz + - Cut1 + - heinz_visualization + - heinz_scoring + - deseq2 + update_time: '2019-01-17' + versions: 1 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Gene functional annotation + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - Read summarisation + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9c7a218993788493 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=9c7a218993788493 + name: Reference-based RNA-Seq data analysis + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - RNA-seq + - deseq2 + - name:STAR + tools: + - fastqc + - gtftobed12 + - Cut1 + - tp_sort_header_tool + - Add_a_column1 + - join1 + - goseq + - ggplot2_heatmap2 + - cutadapt + - rseqc_infer_experiment + - ChangeCase + - rna_star + - multiqc + - featurecounts + - deseq2 + - Filter1 + update_time: '2019-01-17' + versions: 0 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fd156028b09d213a + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=fd156028b09d213a + name: Visualization of RNA-Seq results with Volcano Plot + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - RNA-seq + - visualization + tools: + - volcanoplot + update_time: '2019-01-17' + versions: 0 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c7026cd5578c8678 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c7026cd5578c8678 + name: Small Non-coding RNA Clustering using BlockClust + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - miRNA-seq + - clustering + - classification + tools: + - samtools_sort + - blockclust + - blockbuster + - tp_sort_header_tool + update_time: '2019-01-17' + versions: 0 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + edam_topic: [] + id: 1ffc058273ab357e + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=1ffc058273ab357e + name: 'sRNA-seq Step 2: Differential abundance testing of small RNAs' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - sRNA-seq + tools: + - Filter1 + - deseq2 + - salmon + update_time: '2019-01-17' + versions: 0 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 7734928ebc0a2654 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=7734928ebc0a2654 + name: 'sRNA-seq Step 1: Read pre-processing and removal of artifacts' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - sRNA-seq + - pre-processing + tools: + - fastqc + - fastq_manipulation + - trim_galore + - bedtools_bamtofastq + - samtool_filter2 + - hisat2 + update_time: '2019-01-17' + versions: 0 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Mapping + - Primer removal + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f5be5bcf9b9f171c + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c + name: CLIP-Seq data analysis from pre-processing to motif detection + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - eCLIP + - CLIP-seq + tools: + - fastqc + - __UNZIP_COLLECTION__ + - peakachu + - deeptools_plot_fingerprint + - bctools_extract_alignment_ends + - cutadapt + - rcas + - rna_star + - meme_chip + - Extract genomic DNA 1 + - umi_tools_extract + - tp_awk_tool + - bctools_extract_crosslinked_nucleotides + - bedtools_slopbed + - umi_tools_dedup + - bedtools_genomecoveragebed_bedgraph + - deeptools_multi_bam_summary + - bedtools_sortbed + - deeptools_plot_correlation + - wig_to_bigWig + update_time: '2019-01-17' + versions: 0 +- create_time: '2019-01-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Sequence annotation + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: f026c4b8341ff94c + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=f026c4b8341ff94c + name: De novo transcriptome reconstruction with RNA-Seq + number_of_steps: null + source: https://usegalaxy.eu + tags: + - RNA + - RNA-seq + - assembly + tools: + - fastqc + - trimmomatic + - stringtie + - gffcompare + - deeptools_bam_coverage + - Filter1 + - stringtie_merge + - featurecounts + - deseq2 + - hisat2 + update_time: '2019-01-17' + versions: 0 +- create_time: '2018-10-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d91e715b5e3457d3 + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=d91e715b5e3457d3 + name: Molecular dynamics with GROMACS + number_of_steps: null + source: https://usegalaxy.eu + tags: + - moleculardynamics + tools: + - gmx_nvt + - gmx_npt + - gmx_solvate + - gmx_setup + - gmx_md + - gmx_em + update_time: '2019-01-09' + versions: 9 +- create_time: '2018-08-16' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence trimming + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 44c5999436da5f1e + latest_version: 9 + license: null + link: https://usegalaxy.eu/published/workflow?id=44c5999436da5f1e + name: 1_Demultiplex_eCLIP + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CLIP-Explorer + tools: + - __UNZIP_COLLECTION__ + - umi_tools_extract + - cutadapt + - je_demultiplex + - multiqc + update_time: '2018-12-17' + versions: 9 +- create_time: '2018-08-16' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence trimming + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: a1e09c648d8f1fc7 + latest_version: 8 + license: null + link: https://usegalaxy.eu/published/workflow?id=a1e09c648d8f1fc7 + name: 2_Demultiplex_iCLIP + number_of_steps: null + source: https://usegalaxy.eu + tags: + - CLIP-Explorer + tools: + - __UNZIP_COLLECTION__ + - umi_tools_extract + - cutadapt + - je_demultiplex + - multiqc + update_time: '2018-12-17' + versions: 8 +- create_time: '2018-12-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9858fdf13a522ea8 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=9858fdf13a522ea8 + name: MD Analysis using Bio3D + number_of_steps: null + source: https://usegalaxy.eu + tags: + - analysis + - moleculardynamics + - bio3d + tools: + - bio3d_pca + - bio3d_rmsd + - bio3d_rmsf + update_time: '2018-12-14' + versions: 1 +- create_time: '2018-11-30' + creators: [] + doi: '' + edam_operation: + - Nucleic acid feature detection + edam_topic: [] + id: 7d343d982f1105bf + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf + name: blockclust 1.1.0 complete + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_sort_header_tool + - samtools_sort + - blockclust + - blockbuster + - infernal_cmsearch + - Extract genomic DNA 1 + update_time: '2018-12-10' + versions: 5 +- create_time: '2018-08-17' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Data handling + - Sequence alignment analysis + - RNA-Seq quantification + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c64b219b4031fabd + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=c64b219b4031fabd + name: 'CelSeq2: Single Batch (mm10)' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - umi_tools_extract + - bamFilter + - umi_tools_count + - rna_star + - featurecounts + update_time: '2018-12-05' + versions: 2 +- create_time: '2018-11-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 667d05ae290d11ea + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=667d05ae290d11ea + name: blockclust 1.1.0 clustering + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - samtools_sort + - blockclust + - blockbuster + - tp_sort_header_tool + update_time: '2018-11-27' + versions: 11 +- create_time: '2018-11-19' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: a657b412b37b971b + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a657b412b37b971b + name: Metaproteomics Training Workflow (December 2018) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2018-11-19' + versions: 1 +- create_time: '2018-11-13' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 1706bfa819bbfa89 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89 + name: Metaproteomics training workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2018-11-19' + versions: 3 +- create_time: '2018-11-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f946efa49bd41a43 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=f946efa49bd41a43 + name: MousePG_Workflow3_Novel_peptide_analysis (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_blastp_wrapper + - query_tabular + - tab2fasta + - pep_pointer + - peptidegenomiccoordinate + update_time: '2018-11-13' + versions: 0 +- create_time: '2018-11-13' + creators: [] + doi: '' + edam_operation: + - Peptide database search + - Conversion + edam_topic: [] + id: b89cf3cb6a25c999 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999 + name: MousePG_Workflow2_Database_Search_BlastP_ready (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - query_tabular + - fasta2tab + - mz_to_sqlite + - Grouping1 + - Convert characters1 + - peptide_shaker + - search_gui + update_time: '2018-11-13' + versions: 0 +- create_time: '2018-11-13' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 78e1769f1dcb797b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b + name: 'Copy of imported: Metaproteomics training workflow (imported from uploaded + file) shared by user smehta' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2018-11-13' + versions: 0 +- create_time: '2018-11-13' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: 8fc1ea9e94bc723d + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d + name: Metaproteomics training workflow (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2018-11-13' + versions: 1 +- create_time: '2018-10-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence alignment analysis + - Genome assembly + - Sequence composition calculation + - Sequence comparison + - Primer removal + - Sequence trimming + - Chimera detection + - Read pre-processing + - Gene prediction + - DNA mapping + - Sequence similarity search + - Sequencing quality control + edam_topic: [] + id: 401746888e8b3aa8 + latest_version: 7 + license: null + link: https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8 + name: Workflow for protein sequence generation using MEGAHIT + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trim_galore + - vsearch_dereplication + - fraggenescan + - megahit + - bg_sortmerna + update_time: '2018-11-01' + versions: 7 +- create_time: '2018-10-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence alignment analysis + - Genome assembly + - Sequence composition calculation + - Sequence comparison + - Primer removal + - Sequence trimming + - Chimera detection + - Read pre-processing + - Gene prediction + - DNA mapping + - Sequence similarity search + - Sequencing quality control + edam_topic: [] + id: 9382f9bbbdddb5ad + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad + name: Workflow for protein sequence generation using metaSPAdes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - fasta2tab + - trim_galore + - join1 + - vsearch_dereplication + - tp_cut_tool + - fastq_to_tabular + - fraggenescan + - metaspades + - bg_sortmerna + - tabular_to_fastq + update_time: '2018-11-01' + versions: 4 +- create_time: '2018-10-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5e1b048040ea7535 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=5e1b048040ea7535 + name: Workflow constructed from history 'FASTA to genuine FASTQ' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fasta2tab + - join1 + - tp_cut_tool + - fastq_to_tabular + - tabular_to_fastq + update_time: '2018-10-18' + versions: 1 +- create_time: '2018-10-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence alignment analysis + - Genome assembly + - Sequence composition calculation + - Sequence comparison + - Primer removal + - Sequence trimming + - Chimera detection + - Read pre-processing + - Gene prediction + - DNA mapping + - Sequence similarity search + - Sequencing quality control + edam_topic: [] + id: a8417c63e9e22afb + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb + name: Workflow constructed from history 'Full Option 1' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - trim_galore + - vsearch_dereplication + - fraggenescan + - metaphlan2 + - megahit + - metaspades + - bg_sortmerna + - fastq_combiner + update_time: '2018-10-17' + versions: 2 +- create_time: '2018-10-16' + creators: [] + doi: '' + edam_operation: + - Gene prediction + - Genome assembly + edam_topic: [] + id: 8c7958cb05fba814 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814 + name: Workflow constructed from history 'Final Option 2' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fasta2tab + - join1 + - tp_cut_tool + - fastq_to_tabular + - fraggenescan + - metaspades + - tabular_to_fastq + update_time: '2018-10-16' + versions: 1 +- create_time: '2018-10-16' + creators: [] + doi: '' + edam_operation: + - Gene prediction + - Genome assembly + edam_topic: [] + id: d4a95588e6e50893 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893 + name: Workflow constructed from history 'Final Option 1' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastq_combiner + - fraggenescan + - metaspades + - megahit + update_time: '2018-10-16' + versions: 0 +- create_time: '2018-10-16' + creators: [] + doi: '' + edam_operation: + - Gene prediction + - Genome assembly + edam_topic: [] + id: 534f5fc25bc887ca + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca + name: Workflow constructed from history 'Final Option 0' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fraggenescan + - megahit + update_time: '2018-10-16' + versions: 0 +- create_time: '2018-10-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ad636a8e1763580a + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=ad636a8e1763580a + name: Gxy Intro (P2G - intersect and count) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Grouping1 + - gops_intersect_1 + update_time: '2018-10-10' + versions: 2 +- create_time: '2018-09-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence alignment analysis + - Phylogenetic inference + - Primer removal + - Read pre-processing + - Sequencing quality control + - Taxonomic classification + - Sequence composition calculation + - Sequence comparison + - Phylogenetic tree visualisation + - Sequence trimming + - Visualisation + - Chimera detection + - Conversion + - DNA mapping + - Sequence similarity search + - Phylogenetic tree editing + edam_topic: [] + id: 9cbba5de2cbeeb0f + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f + name: ASaiM - Shotgun workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - metaphlan2krona + - format_metaphlan2_output + - taxonomy_krona_chart + - group_humann2_uniref_abundances_to_go + - export2graphlan + - trim_galore + - vsearch_dereplication + - humann2_genefamilies_genus_level + - metaphlan2 + - humann2 + - graphlan + - bg_sortmerna + - combine_metaphlan2_humann2 + - graphlan_annotate + update_time: '2018-09-26' + versions: 0 +- create_time: '2018-09-22' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation (from molecular sequences) + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: ce21961260fe4351 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=ce21961260fe4351 + name: 16S microbial analysis (Mothur) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Metagenomics + - Mothur + - 16S + tools: + - collapse_dataset + - mothur_heatmap_sim + - mothur_pcoa + - mothur_rarefaction_single + - mothur_align_seqs + - mothur_classify_seqs + - mothur_venn + - taxonomy_krona_chart + - mothur_heatmap_bin + - mothur_make_shared + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_dist_shared + - mothur_dist_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_get_oturep + - mothur_unique_seqs + - mothur_classify_otu + - mothur_taxonomy_to_krona + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - fasttree + - XY_Plot_1 + - mothur_count_groups + - mothur_cluster_split + - mothur_sub_sample + - mothur_pre_cluster + update_time: '2018-09-22' + versions: 1 +- create_time: '2013-10-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c94a1d028357c81e + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e + name: Preparation of a large compound library by merging of chemical databases. + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ctb_change_title + - Cut1 + - ctb_remIons + - bg_uniq + - mergeCols1 + - cat1 + - Grep1 + - ctb_online_data_fetch + - sed_stream_editor + - addValue + - openbabel_compound_convert + - Filter1 + update_time: '2018-09-03' + versions: 4 +- create_time: '2018-02-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b36be9100485e6cd + latest_version: 12 + license: null + link: https://usegalaxy.eu/published/workflow?id=b36be9100485e6cd + name: blockclust_workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - blockbuster + update_time: '2018-08-13' + versions: 12 +- create_time: '2018-01-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Sequence trimming + - Visualisation + - Sequence assembly visualisation + - Sequence assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 579ff83177c5ee09 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09 + name: ASaiM - Metagenomic assembly with MetaSPAdes + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ASaiM + tools: + - fastqc + - quast + - trim_galore + - valet + - metaspades + - multiqc + - bowtie2 + update_time: '2018-08-03' + versions: 3 +- create_time: '2018-01-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Sequence trimming + - Visualisation + - Sequence assembly visualisation + - Sequence assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 1524b189069b42a5 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=1524b189069b42a5 + name: ASaiM - Metagenomic assembly with MEGAHIT + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ASaiM + tools: + - fastqc + - quast + - trim_galore + - valet + - megahit + - multiqc + - bowtie2 + update_time: '2018-08-03' + versions: 4 +- create_time: '2018-01-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence alignment analysis + - Phylogenetic inference + - Primer removal + - Read pre-processing + - Sequencing quality control + - Taxonomic classification + - Sequence composition calculation + - Sequence comparison + - Phylogenetic tree visualisation + - Sequence trimming + - Visualisation + - Chimera detection + - Conversion + - DNA mapping + - Sequence similarity search + - Phylogenetic tree editing + edam_topic: [] + id: c3aa516e78ca4191 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191 + name: ASaiM - Shotgun workflow + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - metaphlan2krona + - format_metaphlan2_output + - taxonomy_krona_chart + - export2graphlan + - trim_galore + - vsearch_dereplication + - humann2_genefamilies_genus_level + - metaphlan2 + - humann2 + - graphlan + - bg_sortmerna + - combine_metaphlan2_humann2 + - graphlan_annotate + update_time: '2018-08-03' + versions: 4 +- create_time: '2018-08-01' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 83a0c1ba280785e6 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=83a0c1ba280785e6 + name: ITS1 (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_chimera_uchime + - mothur_remove_seqs + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_cluster_split + - mothur_make_shared + - mothur_unique_seqs + - mothur_align_seqs + - mothur_classify_otu + - mothur_classify_seqs + - mothur_remove_lineage + - mothur_pre_cluster + update_time: '2018-08-02' + versions: 0 +- create_time: '2018-08-01' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: c55388a8fbfd7381 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c55388a8fbfd7381 + name: CytBCO1 (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - ncbi_blastn_wrapper + - mothur_unique_seqs + update_time: '2018-08-02' + versions: 0 +- create_time: '2018-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b51559006f86db9e + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=b51559006f86db9e + name: Orphan genes (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - filter_by_fasta_ids + - fasta2tab + - cat1 + - tp_sorted_uniq + - comp1 + update_time: '2018-06-26' + versions: 0 +- create_time: '2018-06-26' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: d22dac11eba8c5a3 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3 + name: SwissProt (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - ncbi_blastp_wrapper + - Cut1 + - get_sequences + - get_feature_info + - 'EMBOSS: transeq101' + - uniprot + update_time: '2018-06-26' + versions: 1 +- create_time: '2018-02-16' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Sequence alignment analysis + - Phylogenetic inference (from molecular sequences) + - Local alignment + - Global alignment + - Phylogenetic tree visualisation + - Sequence analysis + - Sequence alignment + edam_topic: [] + id: 2cec6a39cd496f09 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 + name: GeneSeqToFamily (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - blast_parser + - ncbi_blastp_wrapper + - hcluster_sg_parser + - filter_by_fasta_ids + - 'EMBOSS: tranalign100' + - gafa + - treebest_best + - t_coffee + - trimmer + - hcluster_sg + - ncbi_makeblastdb + - 'EMBOSS: transeq101' + update_time: '2018-06-26' + versions: 0 +- create_time: '2018-04-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 329cf724a21f13ec + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=329cf724a21f13ec + name: ASaiM - Shotgun workflow for paired-end data collection + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ASaiM + tools: [] + update_time: '2018-04-30' + versions: 1 +- create_time: '2018-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 358db17bfc1ee330 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=358db17bfc1ee330 + name: Shotgun workflow for paired-end data (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ASaiM + tools: + - fastq_join + update_time: '2018-04-30' + versions: 0 +- create_time: '2018-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1c3adfc77a138ef6 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=1c3adfc77a138ef6 + name: ASaiM - Shotgun workflow for single-end data collection + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ASaiM + tools: [] + update_time: '2018-04-30' + versions: 2 +- create_time: '2018-04-29' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + edam_topic: [] + id: ebaa33538e7ff300 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=ebaa33538e7ff300 + name: Paired-End Workflow constructed from history 'E-MTAB-513' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - bedtools_bamtofastq + - samtools_filter + - hisat2 + update_time: '2018-04-29' + versions: 1 +- create_time: '2018-04-16' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 8de99510abb6ee7c + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=8de99510abb6ee7c + name: From scratch to TADs, PCA and plot (summing up replicates) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - hicexplorer_hiccorrectmatrix + - hicexplorer_hicplottads + - hicexplorer_hicbuildmatrix + - hicexplorer_hicfindtads + - hicexplorer_hicsummatrices + - hicexplorer_hicpca + - bwa_mem + update_time: '2018-04-29' + versions: 2 +- create_time: '2018-02-28' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 59b274da8df01ead + latest_version: 14 + license: null + link: https://usegalaxy.eu/published/workflow?id=59b274da8df01ead + name: 'CelSeq: 2. ReadQC' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - multiqc + - trim_galore + update_time: '2018-03-23' + versions: 14 +- create_time: '2018-02-28' + creators: [] + doi: '' + edam_operation: + - Validation + - Read summarisation + - RNA-Seq quantification + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c6b22fc33b569c8f + latest_version: 19 + license: null + link: https://usegalaxy.eu/published/workflow?id=c6b22fc33b569c8f + name: 'CelSeq: 3. Quantification' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - collection_column_join + - tp_sed_tool + - samtools_stats + - rna_star + - umi_tools_dedup + - multiqc + - featurecounts + update_time: '2018-03-21' + versions: 19 +- create_time: '2018-03-06' + creators: [] + doi: '' + edam_operation: + - Sequencing quality control + edam_topic: [] + id: edbdbe7aa21ceba0 + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=edbdbe7aa21ceba0 + name: 'CelSeq: 1. Demultiplex Collection' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_cat + - je_demultiplex + - umi_tools_extract + update_time: '2018-03-17' + versions: 11 +- create_time: '2018-03-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8483717d51fde024 + latest_version: 20 + license: null + link: https://usegalaxy.eu/published/workflow?id=8483717d51fde024 + name: Workflow constructed from history 'shared workflow' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - mapping-by-sequencing + - mimodd + tools: + - mimodd_vcf_filter + - mimodd_varcall + - mimodd_map + - snpEff + - snpEff_download + - mimodd_varreport + - tp_find_and_replace + - mimodd_varextract + update_time: '2018-03-09' + versions: 20 +- create_time: '2018-01-17' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Taxonomic classification + - Demultiplexing + - Visualisation + - Sequencing quality control + edam_topic: [] + id: 3acfb87be6db2303 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3acfb87be6db2303 + name: QIIME - Illumina Overview tutorial (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ASaiM + tools: + - qiime_split_libraries_fastq + - qiime_pick_open_reference_otus + - qiime_core_diversity + - qiime_count_seqs + - qiime_validate_mapping_file + update_time: '2018-01-17' + versions: 0 +- create_time: '2018-01-17' + creators: [] + doi: '' + edam_operation: + - Sequence database search + - Formatting + - Sequence profile generation + - Statistical calculation + - Phylogenetic analysis + - Format validation + - Sequence motif recognition + - Data retrieval + - Sequencing quality control + - Protein feature detection + - Taxonomic classification + - Demultiplexing + - Database search + - Gene prediction + - Visualisation + - Conversion + - Probabilistic sequence generation + - Sequence generation + - Multiple sequence alignment + edam_topic: [] + id: 58955868b504c60d + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=58955868b504c60d + name: EBI Metagenomics workflow (3.0) (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ASaiM + tools: + - seq_filter_by_id + - trimmomatic + - tp_cat + - hmmer_hmmbuild + - hmmer_hmmsearch + - tp_awk_tool + - fraggenescan + - qiime_pick_closed_reference_otus + - interproscan + - cshl_fastq_to_fasta + update_time: '2018-01-17' + versions: 0 +- create_time: '2017-11-29' + creators: [] + doi: '' + edam_operation: + - Peak calling + - Enrichment analysis + - Gene regulatory network analysis + edam_topic: [] + id: 604b67c8525637bc + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=604b67c8525637bc + name: 'Galaksio use case: Mouse ChIP-seq workflow (imported from uploaded file)' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - ChIP-seq + tools: + - deeptools_plot_fingerprint + - deeptools_multi_bam_summary + - deeptools_plot_correlation + - macs2_callpeak + update_time: '2017-11-29' + versions: 0 +- create_time: '2014-11-13' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Read mapping + - Statistical calculation + edam_topic: [] + id: 2f1ee01aeee2b9f0 + latest_version: 11 + license: null + link: https://usegalaxy.eu/published/workflow?id=2f1ee01aeee2b9f0 + name: PVM-PairedEnds-Bowtie2-Freebayes-GEMINI + number_of_steps: null + source: https://usegalaxy.eu + tags: + - Exome + tools: + - sam_merge2 + - vcfallelicprimitives + - picard_ReorderSam + - snpSift_filter + - gemini_load + - gemini_query + - snpEff + - snpSift_annotate + - picard_MarkDuplicates + - bowtie2 + - freebayes + update_time: '2017-09-22' + versions: 11 +- create_time: '2017-03-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c32d178e6c8e31bd + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=c32d178e6c8e31bd + name: Workflow constructed from history 'Joachims Workflow' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - barchart_gnuplot + - tp_sort_header_tool + update_time: '2017-03-23' + versions: 1 +- create_time: '2016-03-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cde27d06b74ad2fd + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd + name: Secreted Proteins via GO annotation and WoLF PSORT for shCTSB paper + number_of_steps: null + source: https://usegalaxy.eu + tags: + - final + - tested + - published + tools: + - wolf_psort + - bg_uniq + - get_subontology_from + - tp_easyjoin_tool + - tp_cut_tool + - Grep1 + - Convert characters1 + - tp_sorted_uniq + - term_id_vs_term_name + - Filter1 + - comp1 + - uniprot + update_time: '2016-03-18' + versions: 6 +- create_time: '2015-12-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b46b51b2860b63d5 + latest_version: 28 + license: null + link: https://usegalaxy.eu/published/workflow?id=b46b51b2860b63d5 + name: Secreted Proteins via GO annotation and WoLF PSORT for shCTSB paper + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - get_subontology_from + - tp_easyjoin_tool + - Grep1 + - term_id_vs_term_name + - comp1 + - bg_uniq + update_time: '2016-03-11' + versions: 28 +- create_time: '2016-02-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5e09d5e991009cda + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=5e09d5e991009cda + name: add chr at the beginning + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - addValue + - Cut1 + - mergeCols1 + update_time: '2016-02-24' + versions: 1 +- create_time: '2016-02-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6064d1dd87b458be + latest_version: -1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6064d1dd87b458be + name: tgCTS Functional Annotation Clustering + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - get_subontology_from + - tp_easyjoin_tool + - Grep1 + - term_id_vs_term_name + - comp1 + - bg_uniq + update_time: '2016-02-22' + versions: -1 +- create_time: '2016-01-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c9423228df977254 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c9423228df977254 + name: tgCTS Test + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - get_subontology_from + - tp_easyjoin_tool + - Grep1 + - term_id_vs_term_name + - comp1 + - bg_uniq + update_time: '2016-01-27' + versions: 0 +- create_time: '2015-10-12' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Statistical calculation + edam_topic: [] + id: ad609d1a3de251f5 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=ad609d1a3de251f5 + name: PVM-MappedReads-Freebayes-GEMINI + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sam_merge2 + - vcfallelicprimitives + - picard_ReorderSam + - snpSift_filter + - gemini_load + - gemini_query + - snpEff + - snpSift_annotate + - picard_MarkDuplicates + - freebayes + update_time: '2015-10-12' + versions: 0 +- create_time: '2015-10-07' + creators: [] + doi: '' + edam_operation: + - Read mapping + - Data handling + edam_topic: [] + id: 5e4135eeb4972709 + latest_version: 12 + license: null + link: https://usegalaxy.eu/published/workflow?id=5e4135eeb4972709 + name: RNA-seq TopHat2 parameters + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tp_cat + - rseqc_inner_distance + - rseqc_infer_experiment + - tp_awk_tool + - Grep1 + - tp_find_and_replace + - Paste1 + - bowtie2 + - Show beginning1 + update_time: '2015-10-07' + versions: 12 +- create_time: '2014-03-14' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: 1031e4c4f18e020e + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=1031e4c4f18e020e + name: Shuffle Sequences + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - fasta2tab + - 'EMBOSS: shuffleseq87' + - tab2fasta + - addValue + update_time: '2015-07-26' + versions: 3 +- create_time: '2015-07-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d2ef6d4a2189c0a6 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=d2ef6d4a2189c0a6 + name: Workflow constructed from history 'ChipSeq Test Analyses' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Count1 + - cshl_awk_tool + - get_flanks1 + - barchart_gnuplot + - gops_intersect_1 + - tp_replace_in_column + update_time: '2015-07-17' + versions: 0 +- create_time: '2015-07-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f30c8054f064ac9f + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f + name: Galaxy workshop test + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Count1 + - cshl_awk_tool + - charts + - get_flanks1 + - gops_intersect_1 + - tp_replace_in_column + update_time: '2015-07-17' + versions: 1 +- create_time: '2015-02-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f00b862b06093636 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=f00b862b06093636 + name: BlockClustWorkflow_clustering + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - blockclust + - blockbuster + update_time: '2015-06-26' + versions: 0 +- create_time: '2015-02-12' + creators: [] + doi: '' + edam_operation: + - Nucleic acid feature detection + edam_topic: [] + id: 2e1feecca56bb0b8 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8 + name: BlockClustWorkflow_complete + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - blockclust + - blockbuster + - infernal_cmsearch + - Extract genomic DNA 1 + update_time: '2015-06-26' + versions: 0 +- create_time: '2015-06-23' + creators: [] + doi: '' + edam_operation: + - Operation + - Protein feature detection + - Sequence alignment analysis + - Local alignment + - Sequence motif recognition + - Global alignment + - Homology-based gene prediction + - Differential gene expression analysis + - Sequence analysis + - Sequence clustering + - Gene prediction + - Sequence alignment + - Ab-initio gene prediction + edam_topic: [] + id: 33312e5643279e8a + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=33312e5643279e8a + name: Workflow constructed from history 'Genome Annotation Workshop - Results' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tmhmm2 + - seq_filter_by_id + - 'EMBOSS: geecee41' + - ncbi_blastp_wrapper + - blastxml_to_top_descr + - aragorn_trna + - wolf_psort + - seq_composition + - antismash + - megablast_xml_parser + - Grep1 + - interproscan + - Filter1 + - augustus + - blast2go + - fasta_compute_length + update_time: '2015-06-23' + versions: 1 +- create_time: '2015-06-23' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: 0ed8817a90caa2b1 + latest_version: -1 + license: null + link: https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1 + name: Structural annotation of Prokaryotes II + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rmcontamination + - fasta2tab + - tp_cut_tool + - tp_replace_in_column + - Grep1 + - tab2fasta + - build_ucsc_custom_track_1 + - 'EMBOSS: transeq101' + update_time: '2015-06-23' + versions: -1 +- create_time: '2015-06-23' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: 9275d0c90a8713d6 + latest_version: -1 + license: null + link: https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6 + name: Structural annotation of Prokaryotes I + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - glimmer_knowlegde-based + - 'EMBOSS: geecee41' + - trnascan + - aragorn_trna + - rmcontamination + - seq_composition + update_time: '2015-06-23' + versions: -1 +- create_time: '2015-06-12' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 9ac74bd7d1000093 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=9ac74bd7d1000093 + name: Create Full Annotation File + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Add_a_column1 + - cat1 + - bedtools_sortbed + - Cut1 + update_time: '2015-06-12' + versions: 1 +- create_time: '2013-02-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 99c4dce722c023d1 + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=99c4dce722c023d1 + name: Where do the peaks fall? (coverage) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - Add_a_column1 + - barchart_gnuplot + - gops_coverage_1 + - cat1 + - Paste1 + - Summary_Statistics1 + - addValue + - Filter1 + update_time: '2015-06-01' + versions: 3 +- create_time: '2015-05-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Peak calling + - Formatting + - Sequence composition calculation + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 3828466d773e508c + latest_version: 22 + license: null + link: https://usegalaxy.eu/published/workflow?id=3828466d773e508c + name: CGN_ChIP-UT + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - deeptools_bamFingerprint + - deeptools_computeMatrix + - deeptools_heatmapper + - deeptools_bamCorrelate + - deeptools_bamCompare + - deeptools_computeGCBias + - macs2_callpeak + - samtools_flagstat + - deeptools_bamCoverage + - picard_MarkDuplicates + - bowtie2 + - PicardInsertSize + update_time: '2015-05-31' + versions: 22 +- create_time: '2015-05-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 04dbf1e548db74fd + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=04dbf1e548db74fd + name: annotate_deseq2_output + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - tp_easyjoin_tool + - tp_awk_tool + - sed_stream_editor + update_time: '2015-05-18' + versions: 6 +- create_time: '2014-03-22' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: eaf3c4d97399e673 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=eaf3c4d97399e673 + name: Glimmer gene calling with trainingset. + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - glimmer_knowlegde-based + - glimmer_build-icm + - 'EMBOSS: transeq101' + update_time: '2015-05-12' + versions: 0 +- create_time: '2014-03-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3280dc48d768b46a + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3280dc48d768b46a + name: Find secreted proteins with TMHMM and SignalP + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - tmhmm2 + - seq_filter_by_id + - signalp3 + - Filter1 + update_time: '2015-05-12' + versions: 0 +- create_time: '2014-03-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 013cc98f55b01d5d + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=013cc98f55b01d5d + name: Finding 2 genes close to each other + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - Cut1 + - Add_a_column1 + - gops_intersect_1 + - Grouping1 + - ncbi_tblastn_wrapper + update_time: '2015-03-17' + versions: 3 +- create_time: '2015-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a22e5b9c84ae3a34 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=a22e5b9c84ae3a34 + name: fastqc:extract overrepresented sequences + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cshl_awk_tool + update_time: '2015-01-29' + versions: 4 +- create_time: '2014-08-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 64db3c75eb7aac38 + latest_version: 4 + license: null + link: https://usegalaxy.eu/published/workflow?id=64db3c75eb7aac38 + name: genVAST:VC-SamTools-Pipeline + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - snpSift_filter + - bcftools_view + - snpEff + - snpSift_annotate + - samtools_mpileup + update_time: '2014-11-20' + versions: 4 +- create_time: '2014-08-13' + creators: [] + doi: '' + edam_operation: + - Formatting + - Read mapping + edam_topic: [] + id: 7aa0af193da74f60 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=7aa0af193da74f60 + name: genVAST:Pre-processing(Bowtie2) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rgPicardMarkDups + - picard_ReorderSam + - bowtie2 + update_time: '2014-11-13' + versions: 0 +- create_time: '2014-11-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 24ef0d03f58d4fc5 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=24ef0d03f58d4fc5 + name: Workflow constructed from history 'Galaxy Tutorial dataset_1' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - barchart_gnuplot + - Count1 + - gops_intersect_1 + update_time: '2014-11-03' + versions: 1 +- create_time: '2014-09-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 62457d6e5fc3a8af + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=62457d6e5fc3a8af + name: Gemini Postprocessing + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - gemini_lof_sieve + - gemini_recessive_and_dominant + - gemini_roh + - gemini_comp_hets + - gemini_de_novo + - gemini_stats + - gemini_interactions + - gemini_pathways + update_time: '2014-09-30' + versions: 1 +- create_time: '2014-08-13' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + edam_topic: [] + id: ffe93ec81afefd09 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=ffe93ec81afefd09 + name: VariantCalling-FreeBayes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - vcfallelicprimitives + - snpSift_filter + - vt_normalize + - snpEff + - snpSift_annotate + - freebayes + update_time: '2014-09-25' + versions: 5 +- create_time: '2014-09-25' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: c377b21d2be45a57 + latest_version: -1 + license: null + link: https://usegalaxy.eu/published/workflow?id=c377b21d2be45a57 + name: Exome Pre-processing with BWA + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - rgPicardMarkDups + - picard_ReorderSam + - sam_to_bam + - bwa_mem + update_time: '2014-09-25' + versions: -1 +- create_time: '2014-09-24' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + edam_topic: [] + id: 4a89ddab941c6819 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=4a89ddab941c6819 + name: VariantCalling-FreeBayes + number_of_steps: null + source: https://usegalaxy.eu + tags: + - VariantCalling + - SNP + - GWAS + tools: + - vcfallelicprimitives + - snpSift_filter + - snpEff + - snpSift_annotate + - freebayes + update_time: '2014-09-24' + versions: 2 +- create_time: '2014-09-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e1e98a9bf3ff131b + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=e1e98a9bf3ff131b + name: Remove "chr" from beginning of each line + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cshl_sed_tool + update_time: '2014-09-22' + versions: 1 +- create_time: '2014-09-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 086fdfb8049e7cc3 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=086fdfb8049e7cc3 + name: Add "chr" at beginning of each line + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - cshl_awk_tool + update_time: '2014-09-22' + versions: 1 +- create_time: '2014-09-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c76dccb40059001b + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=c76dccb40059001b + name: Proper unique on a column + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - cshl_uniq_tool + - Cut1 + update_time: '2014-09-22' + versions: 0 +- create_time: '2014-09-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3ec327fb030cf8a9 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=3ec327fb030cf8a9 + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - barchart_gnuplot + - Count1 + update_time: '2014-09-22' + versions: 0 +- create_time: '2014-03-03' + creators: [] + doi: '' + edam_operation: + - Formatting + - Read mapping + edam_topic: [] + id: c00fe92f9a579a15 + latest_version: 31 + license: null + link: https://usegalaxy.eu/published/workflow?id=c00fe92f9a579a15 + name: VC-GATK-Pipeline + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - picard_ReorderSam + - rgPicardMarkDups + - gatk2_reduce_reads + - gatk2_indel_realigner + - gatk2_print_reads + - gatk2_haplotype_caller + - gatk2_base_recalibrator + - vcftools_merge + - cshl_cut_tool + - gatk2_realigner_target_creator + - gatk2_variant_apply_recalibration + - gatk2_variant_recalibrator + - bowtie2 + update_time: '2014-08-11' + versions: 31 +- create_time: '2013-10-25' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Gene prediction + - Sequence clustering + edam_topic: [] + id: 0461bbd1f96292e2 + latest_version: 5 + license: null + link: https://usegalaxy.eu/published/workflow?id=0461bbd1f96292e2 + name: GenomeAnnotation and Clusterprediction Prokaryotes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - prokaryotic_ncbi_submission + - rmcontamination + - antismash + - scaffold2fasta + update_time: '2014-03-24' + versions: 5 +- create_time: '2013-11-17' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 4412f7223a557b48 + latest_version: 0 + license: null + link: https://usegalaxy.eu/published/workflow?id=4412f7223a557b48 + name: NGS Variant with freebayes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - fastqc + - sam_merge2 + - picard_ARRG + - bwa_wrapper + - sam_bw_filter + - naive_variant_caller + - sam_to_bam + - allele_counts_1 + - Filter1 + - freebayes + update_time: '2013-11-17' + versions: 0 +- create_time: '2013-10-23' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Gene prediction + - Sequence clustering + edam_topic: [] + id: edbaf66c1e97ebdb + latest_version: 3 + license: null + link: https://usegalaxy.eu/published/workflow?id=edbaf66c1e97ebdb + name: GenomeAnnotation and Clusterprediction Eukaryotes + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - antismash + - eukaryotic_ncbi_submission + - rmcontamination + - scaffold2fasta + update_time: '2013-10-25' + versions: 3 +- create_time: '2013-09-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 97bff2c5f4556a3c + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=97bff2c5f4556a3c + name: methyl bed to bigwig + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Add_a_column1 + - wig_to_bigWig + - Cut1 + - Filter1 + update_time: '2013-09-26' + versions: 2 +- create_time: '2013-08-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e77ebdd18da2f885 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=e77ebdd18da2f885 + name: Quality checks with deepTools + number_of_steps: null + source: https://usegalaxy.eu + tags: + - deepTools + - reads + - QC + - bam + tools: + - computeGCBias + - bamFingerprint + - bamCorrelate_deepTools + update_time: '2013-08-09' + versions: 6 +- create_time: '2013-08-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 39c97fd02d2e57e6 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=39c97fd02d2e57e6 + name: Quality checks with deepTools - without GC bias computation + number_of_steps: null + source: https://usegalaxy.eu + tags: + - fingerprint + - correlation + - bam + - reads + tools: + - bamFingerprint + - bamCorrelate_deepTools + update_time: '2013-08-09' + versions: 1 +- create_time: '2013-08-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a88c14111a87cc01 + latest_version: 6 + license: null + link: https://usegalaxy.eu/published/workflow?id=a88c14111a87cc01 + name: 'deepTools: from 1 BAM file to a meta-gene profile' + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - computeMatrix + - bamCoverage_deepTools + - dt_profiler + update_time: '2013-08-09' + versions: 6 +- create_time: '2013-08-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b2586bf1b8cc96f4 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=b2586bf1b8cc96f4 + name: 'deepTools: from 2 BAMs to a heatmap of log2ratios' + number_of_steps: null + source: https://usegalaxy.eu + tags: + - bam + - reads + - deepTools + - profile + - summaryPlot + - log2ratio + tools: + - bamCompare_deepTools + - heatmapper_deepTools + - Grep1 + - computeMatrix + update_time: '2013-08-09' + versions: 2 +- create_time: '2013-02-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 871f01c2f3fbb687 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=871f01c2f3fbb687 + name: Where do my peaks fall? + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - sort1 + - Count1 + - cshl_awk_tool + - barchart_gnuplot + - cat1 + - wc_gnu + - cshl_uniq_tool + - addValue + - bedtools_intersectbed_bam + update_time: '2013-02-22' + versions: 1 +- create_time: '2013-02-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 668a9f5da768fa30 + latest_version: 2 + license: null + link: https://usegalaxy.eu/published/workflow?id=668a9f5da768fa30 + name: Where do the peaks fall? (coverage) + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Cut1 + - Add_a_column1 + - barchart_gnuplot + - gops_coverage_1 + - cshl_grep_tool + - cat1 + - Summary_Statistics1 + - Paste1 + - addValue + - Filter1 + update_time: '2013-02-21' + versions: 2 +- create_time: '2013-02-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a6ade348ef143292 + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=a6ade348ef143292 + name: MACS-Peaks.xls --> Peaks.bed + number_of_steps: null + source: https://usegalaxy.eu + tags: [] + tools: + - Remove beginning1 + - Cut1 + - Grep1 + - Paste1 + - addValue + update_time: '2013-02-07' + versions: 1 +- create_time: '2024-10-17' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Structure visualisation + - Genome visualisation + - Pathway visualisation + edam_topic: [] + id: 505c826e8c99d7bf + latest_version: 4 + license: MIT + link: https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf + name: EBPhib-big + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - filter_by_fasta_ids + - tp_replace_in_line + - tp_easyjoin_tool + - cat1 + - deeptools_bigwig_compare + - jbrowse2 + - pick_value + - fasta_compute_length + update_time: '2024-10-17' + versions: 4 +- create_time: '2024-10-14' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Structure visualisation + - Genome visualisation + - Pathway visualisation + edam_topic: [] + id: 386d3b300cf05305 + latest_version: 45 + license: MIT + link: https://usegalaxy.org/published/workflow?id=386d3b300cf05305 + name: EBPhib-big_0 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - filter_by_fasta_ids + - tp_easyjoin_tool + - cat1 + - deeptools_bigwig_compare + - jbrowse2 + - pick_value + - fasta_compute_length + update_time: '2024-10-17' + versions: 45 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: d2a5f6a5181aada5 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5 + name: bacterial_genome_annotation (release v1.1.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Genome annotation + edam_topic: [] + id: 5a5d0dc4cd2f1ebd + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=5a5d0dc4cd2f1ebd + name: BREW3R (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - stringtie + - map_param_value + - stringtie_merge + - brew3r_r + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: b6a795834009ce06 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=b6a795834009ce06 + name: Quality and Contamination Control For Genome Assembly (release v1.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Genomics + - fastq + - bacterial-genomics + - taxonomy-assignment + - paired-end + - quality + - ABRomics + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-17' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: aaf8e740b3f8e2c0 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0 + name: amr_gene_detection (release v1.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-10-17' + versions: 1 +- create_time: '2024-10-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ce488732866ba48f + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=ce488732866ba48f + name: EGAPx_VGP_WORKFLOW + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - ncbi_egapx + - __EXTRACT_DATASET__ + - export_remote + update_time: '2024-10-10' + versions: 6 +- create_time: '2024-10-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e93a0522ec3a35e6 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e93a0522ec3a35e6 + name: EGAPx wf + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - ncbi_egapx + - __EXTRACT_DATASET__ + update_time: '2024-10-09' + versions: 1 +- create_time: '2024-10-02' + creators: + - Ross Lazarus + - Anna Syme + - Nadolina Brajuka + - Delphine Lariviere + doi: '' + edam_operation: + - Structure visualisation + - Genome visualisation + - Pathway visualisation + edam_topic: [] + id: 89d3c800d3be6050 + latest_version: 26 + license: MIT + link: https://usegalaxy.org/published/workflow?id=89d3c800d3be6050 + name: TreeValGalAugTwoHaps + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - filter_by_fasta_ids + - Cut1 + - tp_easyjoin_tool + - cat1 + - jbrowse2 + - fasta_compute_length + update_time: '2024-10-09' + versions: 26 +- create_time: '2024-08-27' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Formatting + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7d6617b8316cee19 + latest_version: 15 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7d6617b8316cee19 + name: WGS PE variant calling in haploid system + number_of_steps: null + source: https://usegalaxy.org + tags: + - generic + - VeuPath + - Haploid + tools: + - fastp + - snpSift_extractFields + - collapse_dataset + - lofreq_call + - lofreq_viterbi + - snpEff_build_gb + - samtools_stats + - bcftools_merge + - snpEff + - samtools_view + - picard_MarkDuplicates + - multiqc + - bwa_mem + update_time: '2024-10-07' + versions: 15 +- create_time: '2024-09-27' + creators: + - Marius van den Beek + doi: '' + edam_operation: + - Mapping + - Genome annotation + edam_topic: [] + id: f2f633d2b02b6050 + latest_version: 3 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f2f633d2b02b6050 + name: Repeatmasker_split_gff + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - __EXTRACT_DATASET__ + - split_file_to_collection + - tp_cat + - cat_multiple + - repeatmasker_wrapper + - tp_grep_tool + - bedtools_sortbed + - pick_value + update_time: '2024-10-05' + versions: 3 +- create_time: '2024-10-02' + creators: + - Wendi Bacon + - Pavankumar Videm + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + doi: '' + edam_operation: + - Community profiling + - Sequence alignment + - Loading + edam_topic: [] + id: cdb6c9c7037a95b2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=cdb6c9c7037a95b2 + name: Preprocessing of 10X scRNA-seq data + number_of_steps: null + source: https://usegalaxy.org + tags: + - single-cell + - transcriptomics + tools: + - rna_starsolo + - dropletutils + update_time: '2024-10-04' + versions: 1 +- create_time: '2024-10-03' + creators: + - Paulo Cilas Morais Lyra Junior + doi: '' + edam_operation: [] + edam_topic: [] + id: 0cf9868ebc9ec1dc + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=0cf9868ebc9ec1dc + name: LORIS model build + number_of_steps: null + source: https://usegalaxy.org + tags: + - MachineLearning + - LORIS + - LogisticRegression + - MLModel + tools: + - Remove beginning1 + - sklearn_build_pipeline + - sklearn_ensemble + - plotly_ml_performance_plots + - sklearn_searchcv + update_time: '2024-10-03' + versions: 3 +- create_time: '2024-09-27' + creators: + - Marius van den Beek + doi: '' + edam_operation: + - Genome annotation + edam_topic: [] + id: fb8b997f516288e1 + latest_version: 7 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fb8b997f516288e1 + name: splitfailtest + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - repeatmasker_wrapper + - split_file_to_collection + update_time: '2024-10-03' + versions: 7 +- create_time: '2024-10-03' + creators: + - GalaxyP + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: 2404d5e5b1817825 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=2404d5e5b1817825 + name: Clinical Metaproteomics Quantitation (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:clinicalMP + tools: + - Grouping1 + - Grep1 + - maxquant + - Cut1 + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: 993534c11310a207 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=993534c11310a207 + name: bacterial_genome_annotation (release v1.1.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Statistical calculation + - Data handling + - Taxonomic classification + - Expression analysis + - Sequence contamination filtering + - Cross-assembly + - Sequencing quality control + edam_topic: [] + id: 9f68718f025bed30 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=9f68718f025bed30 + name: Quality and Contamination Control For Genome Assembly (release v1.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Genomics + - fastq + - bacterial-genomics + - taxonomy-assignment + - paired-end + - quality + - ABRomics + - trimming + tools: + - fastp + - tooldistillator_summarize + - est_abundance + - recentrifuge + - kraken2 + - tooldistillator + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - abromics-consortium + - ABRomics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 9ac1e4efe310b3b3 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3 + name: Bacterial Genome Assembly using Shov (release v1.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: ef187f85b103d858 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=ef187f85b103d858 + name: amr_gene_detection (release v1.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: f58c90061c31bd48 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f58c90061c31bd48 + name: 'COVID-19: variation analysis reporting (release v0.3.4)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7e2651e5ed17e3db + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7e2651e5ed17e3db + name: 'COVID-19: variation analysis on ARTIC PE (release v0.5.3)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-01' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + - Phylogenetic tree generation (from molecular sequences) + edam_topic: [] + id: be9bd7286d38c210 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=be9bd7286d38c210 + name: Workflow constructed from history 'Historia de AM - AF' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasttree + - clustalw + update_time: '2024-10-01' + versions: 1 +- create_time: '2024-08-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Taxonomic classification + - Genome assembly + - Sequence composition calculation + - Read mapping + - Aggregation + - Read binning + - Sequence merging + - Sequence contamination filtering + - Sequence trimming + - Visualisation + - Chimera detection + - RNA-Seq analysis + - DNA mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0a61de91bbbe02ad + latest_version: 58 + license: null + link: https://usegalaxy.org/published/workflow?id=0a61de91bbbe02ad + name: 'RNA Virus Discovery: Luke Hanbury' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - krakentools_extract_kraken_reads + - trimmomatic + - vsearch_clustering + - fastq_info + - __DUPLICATE_FILE_TO_COLLECTION__ + - ncbi_blastx_wrapper + - bbtools_bbmap + - blastxml_to_tabular + - fastq_dump + - kraken2 + - tp_grep_tool + - bedtools_bamtofastq + - iuc_pear + - spades_rnaviralspades + - fastq_groomer + update_time: '2024-09-30' + versions: 58 +- create_time: '2024-09-26' + creators: + - Anna Syme + - Torsten Seemann + - Simon Gladman + doi: '' + edam_operation: + - Gene prediction + - Genome annotation + - Genome visualisation + - Coding region prediction + edam_topic: [] + id: 0795dd1d83662bae + latest_version: 0 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=0795dd1d83662bae + name: 'Genome Annotation with Prokka ' + number_of_steps: null + source: https://usegalaxy.org + tags: + - genome-annotation + - GTN + tools: + - prokka + - jbrowse + update_time: '2024-09-27' + versions: 0 +- create_time: '2024-09-26' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: 04c5ea133de3204c + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=04c5ea133de3204c + name: bacterial_genome_annotation (release v1.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Protein feature detection + - Data handling + - Genome assembly + - Sequence motif recognition + - Scaffolding + - Genome annotation + - Nucleic acid feature detection + - Structural variation detection + - Multilocus sequence typing + edam_topic: [] + id: 8cb8a588a0495cfa + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa + name: bacterial_genome_annotation (release v1.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Genomics + - fasta + - ABRomics + - bacterial-genomics + - Annotation + - genome-annotation + tools: + - bakta + - tooldistillator_summarize + - plasmidfinder + - isescan + - integron_finder + - tooldistillator + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - abromics-consortium + - ABRomics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 4d1279007d0137fa + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=4d1279007d0137fa + name: Bacterial Genome Assembly using Shov (release v1.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: 3c177fdf38311118 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=3c177fdf38311118 + name: amr_gene_detection (release v1.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: 516a2181b41af94e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=516a2181b41af94e + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: 90ac9dc2bd9d8092 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=90ac9dc2bd9d8092 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 31ed5a2bcc8da51a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=31ed5a2bcc8da51a + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 56427a9b9c3848bf + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=56427a9b9c3848bf + name: Get Confident Peaks From ChIP_PE replicates (release v1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: affdc1bf42475cc9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=affdc1bf42475cc9 + name: Get Confident Peaks From ChIP_SR replicates (release v1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 89f52c97b3aee938 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=89f52c97b3aee938 + name: RNAseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 1234a128adc25b03 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1234a128adc25b03 + name: RNAseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c69f8c26ec5fb8a6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c69f8c26ec5fb8a6 + name: ChIPseq_SR (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7c4a2339b17a8930 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7c4a2339b17a8930 + name: ATACseq (release v0.17) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: df8b49863e83824d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=df8b49863e83824d + name: ChIPseq_PE (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fce1837144d3a86e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fce1837144d3a86e + name: CUTandRUN (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: c6b6524108f53688 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c6b6524108f53688 + name: 'QIIME2 VI: Diversity metrics and estimations (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - qiime2_core__tools__import + - qiime2__diversity__core_metrics_phylogenetic + - __BUILD_LIST__ + - qiime2__diversity__beta_group_significance + - qiime2__diversity__alpha_group_significance + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: fc5ba945eff33fc6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fc5ba945eff33fc6 + name: QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: 4b5f6b5d4f36e38b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b + name: Taxonomy Profiling and Visualization with Kron (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - kraken2 + - krakentools_kreport2krona + - taxonomy_krona_chart + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Visualisation + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Mapping + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: 3ef08553982f6ffc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc + name: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release + v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - collection_column_join + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - ggplot2_heatmap + - fasta2tab + - tp_replace_in_column + - tp_sorted_uniq + - clustalw + - Remove beginning1 + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - tp_split_on_column + - newick_display + - Count1 + - regexColumn1 + - bedtools_getfastabed + - tp_multijoin_tool + - Cut1 + - fasttree + - tab2fasta + - __FILTER_EMPTY_DATASETS__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + edam_topic: [] + id: 3f252e077e0bcce5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5 + name: Gene-based Pathogen Identification (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:Collection + - name:PathoGFAIR + - name:IWC + - name:microGalaxy + tools: + - abricate + - medaka_consensus_pipeline + - collection_element_identifiers + - split_file_to_collection + - flye + - fasta2tab + - bandage_image + - tab2fasta + - compose_text_param + - tp_find_and_replace + - __BUILD_LIST__ + - param_value_from_file + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 450c2181f89e6b23 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=450c2181f89e6b23 + name: Generate Nx and Size plots for multiple assemblies (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - addName + - collapse_dataset + - Add_a_column1 + - Cut1 + - datamash_ops + - gfastats + - param_value_from_file + - tp_awk_tool + - compose_text_param + - ggplot2_point + - addValue + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: f18e6fa5270fcd37 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=f18e6fa5270fcd37 + name: Generate Nx and Size plots for multiple assemblies (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - addName + - collapse_dataset + - Add_a_column1 + - Cut1 + - datamash_ops + - gfastats + - param_value_from_file + - tp_awk_tool + - compose_text_param + - ggplot2_point + - addValue + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Genome annotation + edam_topic: [] + id: 38f06c4c6dd4eb62 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=38f06c4c6dd4eb62 + name: BREW3R (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - stringtie + - map_param_value + - stringtie_merge + - brew3r_r + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - abromics-consortium + - Abromics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: f4d623a19b32370e + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=f4d623a19b32370e + name: Bacterial Genome Assembly using Shov (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - abromics-consortium + - ABRomics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 0e30324072570abb + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=0e30324072570abb + name: Bacterial Genome Assembly using Shov (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - abromics-consortium + - ABRomics + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Visualisation + - Data handling + - Genome assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 4161cfd67ed94b5d + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d + name: Bacterial Genome Assembly using Shov (release v1.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fastq + - Genomics + - bacterial-genomics + - paired-end + - assembly + - quality + - ABRomics + tools: + - quast + - bandage_info + - tooldistillator_summarize + - shovill + - refseq_masher_matches + - bandage_image + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: fde774a049875466 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=fde774a049875466 + name: amr_gene_detection (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - ABRomics + - abromics-consortium + - Pierre Marin + - Clea Siguret + doi: '' + edam_operation: + - Parsing + - Data handling + - Antimicrobial resistance prediction + edam_topic: [] + id: 2b4b1fe82258f303 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303 + name: amr_gene_detection (release v1.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - fasta + - Genomics + - ABRomics + - antibiotic-resistance + - antimicrobial-resistance-genes + - antimicrobialresistance + - bacterial-genomics + - AMR + - AMR-detection + tools: + - staramr_search + - abricate + - tooldistillator_summarize + - amrfinderplus + - tooldistillator + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: d32392a39c4d6fbf + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf + name: 'QIIME2 IIb: Denoising (sequence quality control) and feature table creation + (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - qiime2__feature_table__summarize + - qiime2__feature_table__tabulate_seqs + - qiime2__metadata__tabulate + - qiime2__dada2__denoise_paired + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 517f307db25e4715 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=517f307db25e4715 + name: 'QIIME2 IIa: Denoising (sequence quality control) and feature table creation + (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - qiime2__feature_table__summarize + - qiime2__dada2__denoise_single + - qiime2__feature_table__tabulate_seqs + - qiime2__metadata__tabulate + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 4ca9319c98be08f8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8 + name: 'QIIME2 Id: Demultiplexed data (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - collection_element_identifiers + - qiime2__demux__summarize + - qiime2_core__tools__import + - __RELABEL_FROM_FILE__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 0dc387dc861bdb61 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61 + name: 'QIIME2 Ic: Demultiplexed data (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - collection_element_identifiers + - qiime2__demux__summarize + - qiime2_core__tools__import + - __RELABEL_FROM_FILE__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: b335f75495dab9b4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b335f75495dab9b4 + name: 'QIIME2 Ib: multiplexed data (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - qiime2__demux__emp_paired + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 685b0de4c31f6695 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=685b0de4c31f6695 + name: 'QIIME2 Ia: multiplexed data (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - qiime2__demux__emp_single + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Matthias Bernt + - UFZ Leipzig + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: 78e60413358273bc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=78e60413358273bc + name: dada2 amplicon analysis pipeline - for paired en (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:amplicon + tools: + - dada2_makeSequenceTable + - __UNZIP_COLLECTION__ + - dada2_seqCounts + - dada2_assignTaxonomyAddspecies + - dada2_filterAndTrim + - __APPLY_RULES__ + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 6fc7497c86ebd8ee + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=6fc7497c86ebd8ee + name: Purging-duplicates-one-haplotype-VGP6b (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 242ef2e9dee35702 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=242ef2e9dee35702 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 7adf904dea83e699 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=7adf904dea83e699 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_grep_tool + - tp_cut_tool + - tp_awk_tool + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: cb4ccd3068819418 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=cb4ccd3068819418 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.7.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_grep_tool + - tp_cut_tool + - tp_awk_tool + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: a737766dd083b280 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a737766dd083b280 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - workflow4metabolomics + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: aeeaf3e06a13bc22 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=aeeaf3e06a13bc22 + name: 'Mass spectrometry: LC-MS preprocessing with XCMS (release v1.0)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - metabolomics + - MS + - LC-MS + - workflow4metabolomics + - xcms + - GTN + tools: + - xcms_merge + - intens_check + - abims_xcms_fillPeaks + - abims_xcms_retcor + - abims_xcms_group + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - xcms_plot_chromatogram + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: b7fe3873ee5e3a02 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=b7fe3873ee5e3a02 + name: Assembly-decontamination-VGP9 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 1b80302437db5937 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=1b80302437db5937 + name: Assembly-decontamination-VGP9 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 5e38c7b36e4918ad + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=5e38c7b36e4918ad + name: Assembly-decontamination-VGP9 (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - ncbi_blastn_wrapper + - parse_mito_blast + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: f1a54b10d4afce8f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=f1a54b10d4afce8f + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 9938a81fb6911412 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=9938a81fb6911412 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fd40e50c9f1545ce + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=fd40e50c9f1545ce + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 9ddfdc9d6cacea88 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=9ddfdc9d6cacea88 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 484f8fcf21d67376 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=484f8fcf21d67376 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 07e873a6d75dfe9f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=07e873a6d75dfe9f + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 3f7550d5d2bf0b96 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=3f7550d5d2bf0b96 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 305fb9f84b053713 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=305fb9f84b053713 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 284150bb1f296378 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=284150bb1f296378 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fa26fd51caea53c7 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=fa26fd51caea53c7 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: d5183b025d0e78dd + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=d5183b025d0e78dd + name: Scaffolding-BioNano-VGP7 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: b1cfa3c239ef2523 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=b1cfa3c239ef2523 + name: Scaffolding-BioNano-VGP7 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - tp_find_and_replace + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 2759eaa8adbd2857 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=2759eaa8adbd2857 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 49e2570e363fda11 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=49e2570e363fda11 + name: kmer-profiling-hifi-VGP1 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 333c5725006e4154 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=333c5725006e4154 + name: kmer-profiling-hifi-VGP1 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: cc50da71cdf6f244 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=cc50da71cdf6f244 + name: Purge-duplicate-contigs-VGP6 (release v0.3.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 426358bd988cb39d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=426358bd988cb39d + name: Purge-duplicate-contigs-VGP6 (release v0.3.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 9ab68c65337b893b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=9ab68c65337b893b + name: Purge-duplicate-contigs-VGP6 (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_cut_tool + - cat1 + - tp_awk_tool + - compose_text_param + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 3db51822f04f4ff7 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7 + name: Scaffolding-HiC-VGP8 (release v0.2.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 28dbbfb3d480f4b1 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1 + name: Scaffolding-HiC-VGP8 (release v0.2.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 3d805d7e0f34c727 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727 + name: Scaffolding-HiC-VGP8 (release v0.2.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: afa89bb0e8966753 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=afa89bb0e8966753 + name: Scaffolding-HiC-VGP8 (release v0.2.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 6341c384ceaf47ed + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed + name: Scaffolding-HiC-VGP8 (release v0.2.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: a4a6d6846c1692f9 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9 + name: Scaffolding with Hi-C data VGP8 (release v0.2.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - compose_text_param + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 4c996921fb6a2334 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4c996921fb6a2334 + name: sra_manifest_to_concatenated_fastqs_ (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: b7c67632a6eabda5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b7c67632a6eabda5 + name: sra_manifest_to_concatenated_fastqs_ (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: af85a2ae187409f4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=af85a2ae187409f4 + name: sra_manifest_to_concatenated_fastqs_ (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 412da1489d6aed45 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=412da1489d6aed45 + name: sra_manifest_to_concatenated_fastqs_ (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: e3366346808b1f55 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e3366346808b1f55 + name: baredSC_2d_logN (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 84112c29ee53a5db + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=84112c29ee53a5db + name: baredSC_1d_logN (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 8d605fbd33003d26 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=8d605fbd33003d26 + name: Assembly-Hifi-only-VGP3 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 1d24cc949c52e475 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=1d24cc949c52e475 + name: Assembly-Hifi-only-VGP3 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: bfef75672b9c3ea4 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=bfef75672b9c3ea4 + name: Assembly-Hifi-only-VGP3 (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: ab0be4897d5355ac + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=ab0be4897d5355ac + name: Assembly-Hifi-only-VGP3 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 7072731b51e16923 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=7072731b51e16923 + name: Assembly-Hifi-only-VGP3 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Matthias Bernt + doi: '' + edam_operation: [] + edam_topic: [] + id: f9048d9678e21f36 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f9048d9678e21f36 + name: MetaProSIP OpenMS 2.8 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - FalseDiscoveryRate + - FeatureFinderMultiplex + - IDMapper + - MSGFPlusAdapter + - DecoyDatabase + - MetaProSIP + - __SORTLIST__ + - PeptideIndexer + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 5c85cd8c56b9f6ab + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5c85cd8c56b9f6ab + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: d02b4d7483936b73 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d02b4d7483936b73 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 305eafecadfa8815 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=305eafecadfa8815 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 6f2e4b4860413153 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6f2e4b4860413153 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: b7ec8d79dc563a93 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b7ec8d79dc563a93 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: e325b97b81b10edb + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e325b97b81b10edb + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 931dd3e6b1fae4f5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=931dd3e6b1fae4f5 + name: Get Confident Peaks From ChIP_PE replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 97dcd7285ebd5817 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=97dcd7285ebd5817 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 462a1176b48eef4a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=462a1176b48eef4a + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: ebe7f93204402a5a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ebe7f93204402a5a + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 170287dcfb9de475 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=170287dcfb9de475 + name: Get Confident Peaks From ChIP_SR replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 3ab66315f50501f0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3ab66315f50501f0 + name: RNAseq_PE (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 87eb1a8ee7a2c984 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=87eb1a8ee7a2c984 + name: RNAseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 3e57e668cf698d19 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3e57e668cf698d19 + name: RNAseq_SR (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: bd2ce9a97c1598df + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bd2ce9a97c1598df + name: RNAseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 27ee9da9121d0522 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=27ee9da9121d0522 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: bae2d6b436cd80ef + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bae2d6b436cd80ef + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3c076bc8551a23d2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3c076bc8551a23d2 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 824730064b5014e5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=824730064b5014e5 + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3673a1ced343d0d0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3673a1ced343d0d0 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 15ea806eaf077617 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=15ea806eaf077617 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 336795e890851c21 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=336795e890851c21 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7b9e17cb1d72d7e4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7b9e17cb1d72d7e4 + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ec66767cab0022ee + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ec66767cab0022ee + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 66e6b41f6c6d52b7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=66e6b41f6c6d52b7 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 148c071f5c5a4586 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=148c071f5c5a4586 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9f1e8e82fb3e2033 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9f1e8e82fb3e2033 + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d2759906e4124964 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d2759906e4124964 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: af71519c81429287 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=af71519c81429287 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 789647a199e563fd + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=789647a199e563fd + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f765c8aa4bc3176c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f765c8aa4bc3176c + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 2d55f489c26f6e97 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2d55f489c26f6e97 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: c027d5f90a9f0c74 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c027d5f90a9f0c74 + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5dd0a672cceb15ec + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5dd0a672cceb15ec + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2f4d5f833aa1c981 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2f4d5f833aa1c981 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c4ac09605633655c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c4ac09605633655c + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 995cc428eace3bc4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=995cc428eace3bc4 + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2957924403998f3a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2957924403998f3a + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 156e245e3d9f22ce + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=156e245e3d9f22ce + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 88e10493f7e6b9d5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=88e10493f7e6b9d5 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a99a938953be5fd6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a99a938953be5fd6 + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1d69ab87c94d68fd + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1d69ab87c94d68fd + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e9f4de639f4cfe02 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e9f4de639f4cfe02 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 917e5a21d51a61ce + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=917e5a21d51a61ce + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5b8497a32bf01c4f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5b8497a32bf01c4f + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 533b1d5d08f9943e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=533b1d5d08f9943e + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c2898d28a3b380d6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c2898d28a3b380d6 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b232caf4a1e1b7ee + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b232caf4a1e1b7ee + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c1ec12905944ca7b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c1ec12905944ca7b + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: eed40b0bd0a233cd + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=eed40b0bd0a233cd + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-12' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 0b62cfa1ff1f0a44 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0b62cfa1ff1f0a44 + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-12' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a63d3ee4a2a4a20b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a63d3ee4a2a4a20b + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: acae55e8f37fea59 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=acae55e8f37fea59 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 444c856f03b6d2a7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=444c856f03b6d2a7 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f7975ae799daf463 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f7975ae799daf463 + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9255c0c9017b139f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9255c0c9017b139f + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: dcf658333596d76a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=dcf658333596d76a + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b78a75ae89ae4c79 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b78a75ae89ae4c79 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 13a1fa4f6daf65cc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=13a1fa4f6daf65cc + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 94ab68d27de2e60f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=94ab68d27de2e60f + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fb588edfd343b24d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fb588edfd343b24d + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: bf3f71a748d88490 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bf3f71a748d88490 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ae1de4267e4da154 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ae1de4267e4da154 + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5ccc7d708e13de60 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5ccc7d708e13de60 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: edf9be785ab9eb65 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=edf9be785ab9eb65 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 914ec4d8fc0022e4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=914ec4d8fc0022e4 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fc130cb411aa7d06 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fc130cb411aa7d06 + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 3eb062db34c0c35b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3eb062db34c0c35b + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-09-05' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: d793885f1a223d9c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d793885f1a223d9c + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-05' + versions: 1 +- create_time: '2024-07-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ca68ad0d7420c615 + latest_version: 17 + license: null + link: https://usegalaxy.org/published/workflow?id=ca68ad0d7420c615 + name: 'KegAlign: Pairwise genome alignment' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - batched_lastz + - kegalign + update_time: '2024-08-30' + versions: 17 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f18946db4c93e88b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f18946db4c93e88b + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a8f633b79b20c760 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a8f633b79b20c760 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 06b489dc859f6e39 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=06b489dc859f6e39 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ae5327f6f30b6138 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ae5327f6f30b6138 + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 506acac8c6a58d5e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=506acac8c6a58d5e + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e9ffad95baa43478 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e9ffad95baa43478 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 60b9910b7bb69f47 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=60b9910b7bb69f47 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1ffc71df8eeed57e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1ffc71df8eeed57e + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 33e827d75a0074df + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=33e827d75a0074df + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7df3246858cd83d1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7df3246858cd83d1 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 098fd236c5e2895d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=098fd236c5e2895d + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 05e86b4df0d14800 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=05e86b4df0d14800 + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d9840d6ecf2b4d2f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d9840d6ecf2b4d2f + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6c95a357a3c1f399 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6c95a357a3c1f399 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 672125473ec700bc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=672125473ec700bc + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6c68072bf72e6c4a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6c68072bf72e6c4a + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 5e565547c5871076 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5e565547c5871076 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-29' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 61a379a8d150bfca + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=61a379a8d150bfca + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-29' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 76fb573f1372ae86 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=76fb573f1372ae86 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f93b5864d6d2659c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f93b5864d6d2659c + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9124c2ec80b35680 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9124c2ec80b35680 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 10c5f3c5cadd7417 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=10c5f3c5cadd7417 + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8bf608c6fd0dabd0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8bf608c6fd0dabd0 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6db96a9c7e4b8d14 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6db96a9c7e4b8d14 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: cd5f803c80875b9c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=cd5f803c80875b9c + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 98a4b90f7fc2bfce + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=98a4b90f7fc2bfce + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 028f1beead539975 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=028f1beead539975 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 45cb3e98b1319c7c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=45cb3e98b1319c7c + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8f392d06d32bdf14 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8f392d06d32bdf14 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 35c022174ce79c1e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=35c022174ce79c1e + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f29d1bcfeaacba04 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f29d1bcfeaacba04 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 172ee5e5bef33d2e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=172ee5e5bef33d2e + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6229546fb8b0eba9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6229546fb8b0eba9 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: bd3bed78eb99e294 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bd3bed78eb99e294 + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a81944fafdc194aa + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a81944fafdc194aa + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-22' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 287a531193a0bf9f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=287a531193a0bf9f + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-22' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a8e5adb65d064641 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a8e5adb65d064641 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3b2bee20f0cfd957 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3b2bee20f0cfd957 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8cbb9936e88d4f49 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8cbb9936e88d4f49 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 62ecc8078a396e9e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=62ecc8078a396e9e + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 93cb976bd4ae546e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=93cb976bd4ae546e + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 527adadecbab2eb6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=527adadecbab2eb6 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 553125cd799e5982 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=553125cd799e5982 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1250ec3ad6199cda + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1250ec3ad6199cda + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c30bfd545ef3a228 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c30bfd545ef3a228 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fcbd4767298488b9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fcbd4767298488b9 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ac87b6133de6a03f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ac87b6133de6a03f + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3b5437544ca3b5dc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3b5437544ca3b5dc + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b19a9163c26f1270 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b19a9163c26f1270 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f5bd2da36ab0a870 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f5bd2da36ab0a870 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8e2b2a40831dfb08 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8e2b2a40831dfb08 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 62c842e67fca5ab7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=62c842e67fca5ab7 + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 2a659b0f87cf7453 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2a659b0f87cf7453 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-15' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 38b0d05e36ca68dc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=38b0d05e36ca68dc + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-15' + versions: 1 +- create_time: '2024-08-12' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + edam_topic: [] + id: 39810594e5c332d5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=39810594e5c332d5 + name: Gigascience_Fusions_demonstration_STS26T-Gent_Workflow (imported from uploaded + file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - CONVERTER_gz_to_uncompressed + - query_tabular + - arriba + - tp_awk_tool + - tab2fasta + - rna_star + - arriba_get_filters + - regex1 + update_time: '2024-08-12' + versions: 0 +- create_time: '2024-08-12' + creators: [] + doi: '' + edam_operation: + - Variant calling + - RNA-Seq analysis + - Transcriptome assembly + - Statistical calculation + - Sequence alignment + - Sequence annotation + edam_topic: [] + id: e336bca259abd474 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e336bca259abd474 + name: Gigascience_Indels_SAV_non-normal_demonstration_STS26T-Gent_Workflow (imported + from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - CONVERTER_gz_to_uncompressed + - filter_tabular + - tp_cat + - stringtie + - fasta2tab + - query_tabular + - regexColumn1 + - fasta_merge_files_and_filter_unique_sequences + - bed_to_protein_map + - hisat2 + - gffcompare + - tab2fasta + - gffcompare_to_bed + - custom_pro_db + - sqlite_to_tabular + - translate_bed + - freebayes + update_time: '2024-08-12' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1d56a0975fca0e99 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1d56a0975fca0e99 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1e0a55635f5b04cf + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1e0a55635f5b04cf + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 4612ec88a57ab9e7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4612ec88a57ab9e7 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c0a108e53ab05b0d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c0a108e53ab05b0d + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: adb86df9061dca2b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=adb86df9061dca2b + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d903c7215a88c79f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d903c7215a88c79f + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c81833a367445f98 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c81833a367445f98 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b1dc9cf054a63be5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b1dc9cf054a63be5 + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 642e71c64a975461 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=642e71c64a975461 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 448a0797f9150198 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=448a0797f9150198 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 12a52ae52e0f1053 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=12a52ae52e0f1053 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 52592de9687fc6de + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=52592de9687fc6de + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 4790266996f12979 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4790266996f12979 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c712b85a55da2a2d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c712b85a55da2a2d + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 51d80a44d7d6fff7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=51d80a44d7d6fff7 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9373050c3ce80d56 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9373050c3ce80d56 + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 572224cc3986f8df + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=572224cc3986f8df + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-08' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: d96bb2d69eb13dcf + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d96bb2d69eb13dcf + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-08' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f1c2d920bd41cebb + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f1c2d920bd41cebb + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5e18bbbe9ff2d9f5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5e18bbbe9ff2d9f5 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 761675cb2c9ad2ef + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=761675cb2c9ad2ef + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 87756e064ab1e28a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=87756e064ab1e28a + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a164d857439a126f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a164d857439a126f + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f0ee8bcd7c8fadca + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f0ee8bcd7c8fadca + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ea4c2defce2f5258 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ea4c2defce2f5258 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1e1d7fac7e241768 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1e1d7fac7e241768 + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ec2f77224324f22e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ec2f77224324f22e + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6dfe0c6e87c6cb7b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6dfe0c6e87c6cb7b + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 07dca0dc191fb1de + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=07dca0dc191fb1de + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 06f3ca70b542556e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=06f3ca70b542556e + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fe4c2791508c56ab + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fe4c2791508c56ab + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 64a329cf75834d6b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=64a329cf75834d6b + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fa226c044fa026ef + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fa226c044fa026ef + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 87c1bdc00b975377 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=87c1bdc00b975377 + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: b2430fa67f6914fc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b2430fa67f6914fc + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-08-01' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a1cb49d176baeae7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a1cb49d176baeae7 + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-08-01' + versions: 1 +- create_time: '2024-07-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d3c2a2622c4499f7 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d3c2a2622c4499f7 + name: Workflow constructed from history 'TTN' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + - snpSift_annotate + - bcftools_view + update_time: '2024-07-28' + versions: 0 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ba5889301928907f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ba5889301928907f + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a17af8b7b2b39c1a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a17af8b7b2b39c1a + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 85011076892808e0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=85011076892808e0 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 063173d36c254105 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=063173d36c254105 + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ca36eebd59575df3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ca36eebd59575df3 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 472f73c3e81da1d9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=472f73c3e81da1d9 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 99ee567c092fb34c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=99ee567c092fb34c + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8095deba606ebd5e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8095deba606ebd5e + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: efe7ca87323773c0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=efe7ca87323773c0 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e7fa48d7fd40908b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e7fa48d7fd40908b + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 92aab10842ff610d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=92aab10842ff610d + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 70f9c7cc75a1d3c0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=70f9c7cc75a1d3c0 + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5a55d9bd9701b1ce + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5a55d9bd9701b1ce + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 424acfc2ded46f9f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=424acfc2ded46f9f + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 4a01263e3d4b4edb + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4a01263e3d4b4edb + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9763787d7b102f39 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9763787d7b102f39 + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: ef8d3e19e09b9246 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ef8d3e19e09b9246 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-07-25' + versions: 1 +- create_time: '2024-07-25' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 7e275e09c2bb81b9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7e275e09c2bb81b9 + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-07-25' + versions: 1 +- create_time: '2022-11-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 7022c4d9af725e5c + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c + name: RNA-seq Footitt HISAT-featurecounts + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gtftobed12 + - samtools_idxstats + - fasterq_dump + - rseqc_read_distribution + - rseqc_geneBody_coverage + - cutadapt + - multiqc + - featurecounts + - hisat2 + update_time: '2024-07-24' + versions: 3 +- create_time: '2024-03-23' + creators: + - Amy Heather Fitzpatrick + doi: '' + edam_operation: + - Sequence database search + - Statistical calculation + - Sequence alignment analysis + - De-novo assembly + - Read mapping + - Coding region prediction + - Genome annotation + - Generation + - Sequencing quality control + - Data handling + - Taxonomic classification + - Genome assembly + - Genome indexing + - Sequence composition calculation + - Database search + - Sequence merging + - Transcriptome assembly + - Data retrieval + - Gene prediction + - Sequence alignment + edam_topic: [] + id: e1d2a3bdc900af09 + latest_version: 66 + license: null + link: https://usegalaxy.org/published/workflow?id=e1d2a3bdc900af09 + name: RNA Virus Discovery + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - bamtools_split_mapped + - bwa + - fastq_dump + - kraken2 + - prokka + - orfipy + - bedtools_bamtofastq + - bg_diamond_makedb + - iuc_pear + - datasets_download_genome + - bg_diamond + - spades_rnaviralspades + - fastq_groomer + update_time: '2024-07-22' + versions: 66 +- create_time: '2024-07-19' + creators: + - '' + - "B\xE9r\xE9nice Batut" + doi: '' + edam_operation: + - Variant calling + - Analysis + - Visualisation + - Deposition + - DNA barcoding + edam_topic: [] + id: 4faff660f6defa10 + latest_version: 0 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4faff660f6defa10 + name: Building an amplicon sequence variant (ASV) table from 16S data using DADA2 + number_of_steps: null + source: https://usegalaxy.org + tags: + - microbiome + tools: + - dada2_makeSequenceTable + - __UNZIP_COLLECTION__ + - collection_element_identifiers + - phyloseq_from_dada2 + - tp_replace_in_line + - dada2_seqCounts + - Add_a_column1 + - dada2_assignTaxonomyAddspecies + - tp_replace_in_column + - __SORTLIST__ + - dada2_filterAndTrim + - tp_head_tool + - cat1 + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2024-07-19' + versions: 0 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8e918c12d2f0d1fc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8e918c12d2f0d1fc + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: adbed5c956a71543 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=adbed5c956a71543 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b86d24a103181742 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b86d24a103181742 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9c688a2fc8d1bf4e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9c688a2fc8d1bf4e + name: ChIPseq_SR (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 91806144e90637e8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=91806144e90637e8 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2b5346b94358df88 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2b5346b94358df88 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 00bc4e99626da1ba + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=00bc4e99626da1ba + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: cbbd7e95041d9429 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=cbbd7e95041d9429 + name: ATACseq (release v0.16) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 4b7daa3c73c8ef30 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4b7daa3c73c8ef30 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1cbd946c4cc0e7b9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1cbd946c4cc0e7b9 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9da9ddae8d5dc92f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9da9ddae8d5dc92f + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 64af2cd469fee16a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=64af2cd469fee16a + name: ChIPseq_PE (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1d8227ad3f3651a0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1d8227ad3f3651a0 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c0746df296544a3a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c0746df296544a3a + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a2046dd883227b49 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a2046dd883227b49 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e9927c058ec0661f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e9927c058ec0661f + name: CUTandRUN (release v0.12) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 80785485eb32e062 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=80785485eb32e062 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 0dc0773c9af30002 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0dc0773c9af30002 + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-07-18' + versions: 1 +- create_time: '2024-07-09' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 03258e0321162584 + latest_version: 28 + license: null + link: https://usegalaxy.org/published/workflow?id=03258e0321162584 + name: EdgeR UQ + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - edger + update_time: '2024-07-17' + versions: 28 +- create_time: '2022-09-01' + creators: [] + doi: '' + edam_operation: + - Peak calling + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + edam_topic: [] + id: a0693c1cf1100a1a + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=a0693c1cf1100a1a + name: 5hmC-Demo + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie2 + - bedtools_bamtofastq + - macs2_callpeak + - samtools_rmdup + update_time: '2024-07-12' + versions: 3 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 570172fbcf865e1d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=570172fbcf865e1d + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 02e29499b946f3bb + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=02e29499b946f3bb + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: de24e5678f541584 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=de24e5678f541584 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: dbc650d226e89013 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=dbc650d226e89013 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7fb4dae5daab0522 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7fb4dae5daab0522 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: bb25ac3ba4863424 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bb25ac3ba4863424 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9edc78f665579559 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9edc78f665579559 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: dc006ebf798f1f2f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=dc006ebf798f1f2f + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 091f788edad78956 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=091f788edad78956 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c20a68563e80d401 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c20a68563e80d401 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ddf222b797082436 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ddf222b797082436 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b0b6dfa166b0d873 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b0b6dfa166b0d873 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 11f28984c6b94cdc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=11f28984c6b94cdc + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-11' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: caa7b09601ea6cfe + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=caa7b09601ea6cfe + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-07-11' + versions: 1 +- create_time: '2024-07-04' + creators: + - Giovanna Teixeira Tuchinski + doi: '' + edam_operation: + - Genome visualisation + - Operation + - Genome assembly + - Mapping + - Sequence annotation + - Homology-based gene prediction + - Scaffolding + - Sequence assembly validation + - Transcriptome assembly + - Gene prediction + - Ab-initio gene prediction + edam_topic: [] + id: ec3cc032a90c44f1 + latest_version: 19 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1 + name: Plant Genome Structural Annotation and NLR Annotation + number_of_steps: null + source: https://usegalaxy.org + tags: + - Genome + - Plant + - DNA + - QualityAssessment + - genome-annotation + tools: + - gffread + - filter_by_fasta_ids + - fasta-stats + - bedtools_intersectbed + - jbrowse + - export_remote + - augustus + - busco + update_time: '2024-07-10' + versions: 19 +- create_time: '2024-07-09' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: e790587f0a61fbad + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=e790587f0a61fbad + name: 'DESeq: 2 Replicates Weeks 1 and 2 ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deg_annotate + - deseq2 + update_time: '2024-07-09' + versions: 5 +- create_time: '2024-07-08' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: fc2b48600853f3ea + latest_version: 0 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=fc2b48600853f3ea + name: Assembly-decontamination-VGP9 + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2024-07-08' + versions: 0 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5199f404ad7ecef8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5199f404ad7ecef8 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 87d7a69106ca663d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=87d7a69106ca663d + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c57f70d686b6062e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c57f70d686b6062e + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 885f0e66fa6b8790 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=885f0e66fa6b8790 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 97c20a819394e381 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=97c20a819394e381 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: af5d714396856e9a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=af5d714396856e9a + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 75324d68ed124ff5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=75324d68ed124ff5 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1f00e44f590b8369 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1f00e44f590b8369 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 4ca8b023f9a33440 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4ca8b023f9a33440 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ee27581327d147da + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ee27581327d147da + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: cd4d88429f096fbc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=cd4d88429f096fbc + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e5f79f576548f7c5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e5f79f576548f7c5 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: c82a73c85add7ec4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c82a73c85add7ec4 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-04' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: acb49fe14ae16fe9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=acb49fe14ae16fe9 + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-07-04' + versions: 1 +- create_time: '2024-07-03' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Visualisation + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Mapping + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: 2d3063882d8239ff + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2d3063882d8239ff + name: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - collection_column_join + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - ggplot2_heatmap + - fasta2tab + - tp_replace_in_column + - tp_sorted_uniq + - clustalw + - Remove beginning1 + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - tp_split_on_column + - newick_display + - Count1 + - regexColumn1 + - bedtools_getfastabed + - tp_multijoin_tool + - Cut1 + - fasttree + - tab2fasta + - __FILTER_EMPTY_DATASETS__ + - regex1 + update_time: '2024-07-03' + versions: 1 +- create_time: '2024-07-03' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: [] + edam_topic: [] + id: e55593af91337a05 + latest_version: 0 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e55593af91337a05 + name: PathoGFAIR (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:microGalaxy + - name:IWC + - name:PathoGFAIR + - name:Nanopore + - name:Collection + tools: [] + update_time: '2024-07-03' + versions: 0 +- create_time: '2024-07-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 47ea095ef2c4a417 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=47ea095ef2c4a417 + name: Copy of Make Ensembl GTF compatible with Cufflinks + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - addValue + - Paste1 + - Cut1 + - mergeCols1 + update_time: '2024-07-02' + versions: 0 +- create_time: '2024-06-28' + creators: + - New England Biolabs + - Adrian Reich + - Bradley W. Langhorst + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence composition calculation + - Mapping + - Read mapping + - Validation + - Sequence contamination filtering + - Sequence file editing + - Sequencing quality control + edam_topic: [] + id: cdea4f88ccbd155f + latest_version: 1 + license: AGPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=cdea4f88ccbd155f + name: FFPE QC + number_of_steps: null + source: https://usegalaxy.org + tags: + - DNA + - NEBNext + - QualityAssessment + tools: + - fastqc + - fastp + - tasmanian_mismatch + - bedtools_genomecoveragebed + - picard_CASM + - picard_CollectInsertSizeMetrics + - samtools_flagstat + - picard_CollectGcBiasMetrics + - picard_MarkDuplicates + - multiqc + - bowtie2 + - seqtk_sample + update_time: '2024-06-29' + versions: 1 +- create_time: '2024-06-18' + creators: + - New England Biolabs + - Adrian Reich + - Bradley W. Langhorst + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence composition calculation + - Mapping + - Read mapping + - Validation + - Sequence contamination filtering + - Sequence file editing + - Sequencing quality control + edam_topic: [] + id: 1ddabc7d272dc702 + latest_version: 12 + license: AGPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=1ddabc7d272dc702 + name: FFPE DNA workflow QC + number_of_steps: null + source: https://usegalaxy.org + tags: + - DNA + - NEBNext + - QualityAssessment + tools: + - fastqc + - fastp + - tasmanian_mismatch + - bedtools_genomecoveragebed + - picard_CASM + - picard_CollectInsertSizeMetrics + - samtools_flagstat + - picard_CollectGcBiasMetrics + - picard_MarkDuplicates + - multiqc + - bowtie2 + - seqtk_sample + update_time: '2024-06-28' + versions: 12 +- create_time: '2024-04-04' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 53fea86eb74c224b + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=53fea86eb74c224b + name: ATAC_seq_mapping_BoF + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastp + - samtools_view + - __FILTER_FAILED_DATASETS__ + - bwa + - multiqc + update_time: '2024-06-27' + versions: 4 +- create_time: '2024-06-27' + creators: + - Matthias Bernt + doi: '' + edam_operation: [] + edam_topic: [] + id: 0775ff66d1bc04b5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5 + name: MetaProSIP OpenMS 2.8 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - FalseDiscoveryRate + - FeatureFinderMultiplex + - IDMapper + - MSGFPlusAdapter + - DecoyDatabase + - MetaProSIP + - __SORTLIST__ + - PeptideIndexer + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 626260e3c3ee5c08 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=626260e3c3ee5c08 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 5361db01e3b6cc0c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5361db01e3b6cc0c + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 375f5142c207a768 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=375f5142c207a768 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 7090bb14a7af15bd + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7090bb14a7af15bd + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: cfa7c3d7e69e91d7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=cfa7c3d7e69e91d7 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: d2dec03b33af1b2f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d2dec03b33af1b2f + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: e31abcc04c5c69bc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e31abcc04c5c69bc + name: Get Confident Peaks From ChIP_PE replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: fff1a5c7475b3eeb + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fff1a5c7475b3eeb + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: c66e2738f37a8c16 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c66e2738f37a8c16 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 0b85fb10ed25d34e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0b85fb10ed25d34e + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 9192807702bc3de2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9192807702bc3de2 + name: Get Confident Peaks From ChIP_SR replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ea5d2401f6711dff + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ea5d2401f6711dff + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 313d50268e1e22e4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=313d50268e1e22e4 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 96cdba1fe599ada8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=96cdba1fe599ada8 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: cf3320614654adfe + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=cf3320614654adfe + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: df24d76ebf13e3c1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=df24d76ebf13e3c1 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e58a87508a337b91 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e58a87508a337b91 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b3c8d64eca750ecf + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b3c8d64eca750ecf + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2d6d74294e911fa3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2d6d74294e911fa3 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 0d47009eb2d7bdc1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0d47009eb2d7bdc1 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 150e288c2c2fe9e9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=150e288c2c2fe9e9 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 58eeb06f911e8410 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=58eeb06f911e8410 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ace738014a7278b0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ace738014a7278b0 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 5355f0c34d5a9f40 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5355f0c34d5a9f40 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-27' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: d830ca239e385b9d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d830ca239e385b9d + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-06-27' + versions: 1 +- create_time: '2024-06-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d82db9c29b998f22 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d82db9c29b998f22 + name: Workflow para bilogia de sistemas + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - fasterq_dump + - cutadapt + - __FLATTEN__ + - rna_star + - multiqc + - featurecounts + update_time: '2024-06-26' + versions: 0 +- create_time: '2024-06-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d2b994833b79d2cb + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=d2b994833b79d2cb + name: quantumpsp+rebuild+em--DEMO + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pulchra + - __EXTRACT_DATASET__ + - qiskit_xyz2pdb + - gmx_em + - gmx_setup + - interactive_tool_qiskit_jupyter_notebook + - gmx_editconf + update_time: '2024-06-26' + versions: 2 +- create_time: '2024-06-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: d2f7fd589a91124a + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=d2f7fd589a91124a + name: Official Workflow Version1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cutadapt + - htseq_count + - rna_star + - multiqc + - deseq2 + update_time: '2024-06-25' + versions: 6 +- create_time: '2024-06-25' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: 8f5904693b5f74f4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4 + name: Taxonomy Profiling and Visualization with Krona + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - kraken2 + - krakentools_kreport2krona + - taxonomy_krona_chart + update_time: '2024-06-25' + versions: 1 +- create_time: '2024-06-25' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + edam_topic: [] + id: cce88bc57b180d09 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=cce88bc57b180d09 + name: Gene-based Pathogen Identification + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:Collection + - name:PathoGFAIR + - name:IWC + - name:microGalaxy + tools: + - abricate + - medaka_consensus_pipeline + - collection_element_identifiers + - split_file_to_collection + - flye + - fasta2tab + - bandage_image + - tab2fasta + - compose_text_param + - tp_find_and_replace + - __BUILD_LIST__ + - param_value_from_file + update_time: '2024-06-25' + versions: 1 +- create_time: '2024-06-25' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Variant calling + - Pairwise sequence alignment + edam_topic: [] + id: 38911ba6f66d80f6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6 + name: Allele-based Pathogen Identification + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - clair3 + - CONVERTER_gz_to_uncompressed + - table_compute + - snpSift_filter + - Count1 + - Remove beginning1 + - Cut1 + - snpSift_extractFields + - collapse_dataset + - samtools_coverage + - regexColumn1 + - tp_cut_tool + - bcftools_norm + - tp_head_tool + - samtools_depth + - Paste1 + - minimap2 + - bcftools_consensus + update_time: '2024-06-25' + versions: 1 +- create_time: '2024-06-25' + creators: + - "B\xE9r\xE9nice Batut" + - Engy Nasr + - Paul Zierep + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Visualisation + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: 574e42683dc3961b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=574e42683dc3961b + name: Nanopore Preprocessing + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:Nanopore + - name:IWC + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - krakentools_extract_kraken_reads + - collection_column_join + - Cut1 + - collapse_dataset + - Add_a_column1 + - __FILTER_FAILED_DATASETS__ + - bamtools_split_mapped + - regexColumn1 + - kraken2 + - porechop + - Grep1 + - minimap2 + - multiqc + update_time: '2024-06-25' + versions: 1 +- create_time: '2019-05-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Validation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 1f4dc0488f0554c6 + latest_version: 12 + license: null + link: https://usegalaxy.org/published/workflow?id=1f4dc0488f0554c6 + name: NGS Pipeline for Paired End Reads (R1 and R2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - bamFilter + - vcffilter2 + - bamleftalign + - multiqc + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2024-06-20' + versions: 12 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: f794b4b9bb990c80 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f794b4b9bb990c80 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 918863756ce93725 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=918863756ce93725 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: e53b695ff681b675 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e53b695ff681b675 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 6960b8f6c98a9b9e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6960b8f6c98a9b9e + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 958b64b05011d8c0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=958b64b05011d8c0 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: ab490af27c9ccc80 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ab490af27c9ccc80 + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 91ed290805f590de + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=91ed290805f590de + name: Get Confident Peaks From ChIP_PE replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 28b2550248a54d74 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=28b2550248a54d74 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 25b8b5af30042d76 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=25b8b5af30042d76 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 2b6245843e632c05 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2b6245843e632c05 + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 019be65613876562 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=019be65613876562 + name: Get Confident Peaks From ChIP_SR replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 162fda90525220de + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=162fda90525220de + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 875ff758068e1c2f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=875ff758068e1c2f + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 442949862ba62462 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=442949862ba62462 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9e9a027e0c294a79 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9e9a027e0c294a79 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 17f3d7e52777d2e8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=17f3d7e52777d2e8 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a4a56efb37d845bf + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a4a56efb37d845bf + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9990b6e2facf6dca + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9990b6e2facf6dca + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 899f4f371b4c958c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=899f4f371b4c958c + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1829c91a30138721 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1829c91a30138721 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7757cd56fa4d060c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7757cd56fa4d060c + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c1339c998a55431c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c1339c998a55431c + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3d0ba2f11f370e05 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3d0ba2f11f370e05 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a04c25ac243002ad + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a04c25ac243002ad + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-06-20' + versions: 1 +- create_time: '2024-06-20' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 712234790045e58c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=712234790045e58c + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-06-20' + versions: 1 +- create_time: '2015-07-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5b72ffcea967494f + latest_version: 17 + license: null + link: https://usegalaxy.org/published/workflow?id=5b72ffcea967494f + name: 'Abundance NrD Analysis Workflow: 5 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Count1 + - Cut1 + - Add_a_column1 + - Filter1 + update_time: '2024-06-14' + versions: 17 +- create_time: '2015-07-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 03744158aa2c4149 + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=03744158aa2c4149 + name: 'Persistence NrD Analysis Workflow: 5 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Count1 + - Cut1 + - Add_a_column1 + - Filter1 + update_time: '2024-06-14' + versions: 11 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: c478d8de43a3f30f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c478d8de43a3f30f + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: a3ff7dbfadbd96e2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a3ff7dbfadbd96e2 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: c07476a937b4e52e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c07476a937b4e52e + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: f8d85cda81baa77d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f8d85cda81baa77d + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 769ec5a187095b38 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=769ec5a187095b38 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 357225c624e796b5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=357225c624e796b5 + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 8db9ccf14567d9ba + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8db9ccf14567d9ba + name: Get Confident Peaks From ChIP_PE replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: b93a475af82a3d36 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b93a475af82a3d36 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 8ae311282a0d27a1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8ae311282a0d27a1 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 8a15bda6ce7a63ec + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8a15bda6ce7a63ec + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 226b506d1fc30e96 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=226b506d1fc30e96 + name: Get Confident Peaks From ChIP_SR replicates (release v1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b893662378ed3da0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b893662378ed3da0 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 77d1505c0dd65e26 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=77d1505c0dd65e26 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f9cd2289c007f103 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f9cd2289c007f103 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: dff3cf6921b3d4d6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=dff3cf6921b3d4d6 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 59007e2bc9c807ee + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=59007e2bc9c807ee + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 46e718fb8eeb4d54 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=46e718fb8eeb4d54 + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f733ad0a6cc50cb9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f733ad0a6cc50cb9 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3823773ef4ecaaf4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3823773ef4ecaaf4 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1010a9b57c77239c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1010a9b57c77239c + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 607d1683d6e26cef + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=607d1683d6e26cef + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f3b417763495221b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f3b417763495221b + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1dd63a7b4c6f4c83 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1dd63a7b4c6f4c83 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: ed0a5c1bbd978c34 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ed0a5c1bbd978c34 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-06-13' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: caee1b54c00784b4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=caee1b54c00784b4 + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-06-13' + versions: 1 +- create_time: '2024-05-30' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Formatting + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 57f4c6f5206edfcb + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=57f4c6f5206edfcb + name: Copy-(uncompressedgenome)#2 CA_100323_hsa.T2T_hs1.fa_CamillePruitt + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastp + - picard_NormalizeFasta + - rbc_mirdeep2_quantifier + - rbc_mirdeep2 + - rbc_mirdeep2_mapper + update_time: '2024-06-07' + versions: 7 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: f5200b7bcceed5d6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f5200b7bcceed5d6 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 9b384b774485b2f2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9b384b774485b2f2 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: ef6036efe8a03a12 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ef6036efe8a03a12 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: f8ed1ae9d501bb87 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f8ed1ae9d501bb87 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 19ce6cf93298e268 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=19ce6cf93298e268 + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 63b0ce2faec558d5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=63b0ce2faec558d5 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: c9474fcce2a21188 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c9474fcce2a21188 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 85e2a1d6b1d4e3d7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=85e2a1d6b1d4e3d7 + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ce815d36cbb57304 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ce815d36cbb57304 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6e47a35cc5f2bdce + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6e47a35cc5f2bdce + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 47a2458ee9d57b24 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=47a2458ee9d57b24 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9eb29b71d7effefc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9eb29b71d7effefc + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: cd824d8631d6a55e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=cd824d8631d6a55e + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d00ac64dcd07f91a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d00ac64dcd07f91a + name: ATACseq (release v0.15) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 89f48993bb8f94bd + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=89f48993bb8f94bd + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8756aabc654b1050 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8756aabc654b1050 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 75e23bc4e1ac2f5b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=75e23bc4e1ac2f5b + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6ea1bd64873b6c18 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6ea1bd64873b6c18 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: bcb798fb718968ce + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bcb798fb718968ce + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 30ba39be60ec29be + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=30ba39be60ec29be + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-06-06' + versions: 1 +- create_time: '2024-06-06' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 463ffaa860195d64 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=463ffaa860195d64 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-06-06' + versions: 1 +- create_time: '2023-12-18' + creators: + - CSBL + doi: '' + edam_operation: + - Protein feature detection + - Genome assembly + - De-novo assembly + - Sequence motif recognition + - Coding region prediction + - Scaffolding + - Differential gene expression analysis + - Genome annotation + - Transcriptome assembly + - Sequence clustering + - Cross-assembly + - Mapping assembly + - Gene prediction + - Filtering + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: c451e4dca9981ed0 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0 + name: CSBL-GAA-ONT + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - flye + - filtlong + - prokka + - antismash + - interproscan + - busco + update_time: '2024-06-05' + versions: 4 +- create_time: '2024-06-04' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 868acaf49d0743ec + latest_version: 0 + license: MIT + link: https://usegalaxy.org/published/workflow?id=868acaf49d0743ec + name: RNAseq_PE + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + - cloud-costs + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2024-06-04' + versions: 0 +- create_time: '2024-06-03' + creators: [] + doi: '' + edam_operation: + - Read mapping + - Data handling + edam_topic: [] + id: 3df85f2e7e157514 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=3df85f2e7e157514 + name: SRAtoBowtie2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_dump + - bowtie2 + update_time: '2024-06-04' + versions: 7 +- create_time: '2024-05-29' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e67b6da41e1e6932 + latest_version: 5 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e67b6da41e1e6932 + name: Copy of Variant analysis on WGS PE data shared by user ksuderman + number_of_steps: null + source: https://usegalaxy.org + tags: + - mpxv + - generic + - cloud-costs + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - basil + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-05-31' + versions: 5 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: d485bf21a5069fe4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d485bf21a5069fe4 + name: sra_manifest_to_concatenated_fastqs_ (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: d1ca40dd7e591025 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d1ca40dd7e591025 + name: sra_manifest_to_concatenated_fastqs_ (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 889b394b38b259eb + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=889b394b38b259eb + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: c75acc1ab44c121f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c75acc1ab44c121f + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 672ca09dce4b0dc3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=672ca09dce4b0dc3 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 05ef809e2b11154c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=05ef809e2b11154c + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 405dc14eb02ff234 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=405dc14eb02ff234 + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 0dec1b9dbbb2f425 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0dec1b9dbbb2f425 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 3fdd7a7907233d58 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3fdd7a7907233d58 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 2b820beaeb49dd64 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2b820beaeb49dd64 + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c96b12be162f744b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c96b12be162f744b + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 76d5143860fac947 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=76d5143860fac947 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 96ae2544e22d34c5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=96ae2544e22d34c5 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 52e2b69787ca7a17 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=52e2b69787ca7a17 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2078abc4c99c3344 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2078abc4c99c3344 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a8a38b594183db2b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a8a38b594183db2b + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 68495cc8ec3d46df + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=68495cc8ec3d46df + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 32c769241ffce3d1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=32c769241ffce3d1 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-30' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: ef17168194722023 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ef17168194722023 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-05-30' + versions: 1 +- create_time: '2024-05-28' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d817e98cef94bc96 + latest_version: 0 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d817e98cef94bc96 + name: Variant analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.org + tags: + - mpxv + - generic + - cloud-costs + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-05-28' + versions: 0 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a97c694b3298ae44 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a97c694b3298ae44 + name: sra_manifest_to_concatenated_fastqs_ (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 7454015793c4adc9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7454015793c4adc9 + name: sra_manifest_to_concatenated_fastqs_ (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 36c885b0bc829da3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=36c885b0bc829da3 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: a124d41da896779c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a124d41da896779c + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 13d9db3715f32b37 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=13d9db3715f32b37 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: adca3f2ca63730fe + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=adca3f2ca63730fe + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 7e56bee496344ddc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7e56bee496344ddc + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 46894456a9bec601 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=46894456a9bec601 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 68be9cfc0c58cb44 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=68be9cfc0c58cb44 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: eab7347464872b4c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=eab7347464872b4c + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e1aad86fdf9e6616 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e1aad86fdf9e6616 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5532e6f775adb0d7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5532e6f775adb0d7 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ee3b8d7ba29da11c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ee3b8d7ba29da11c + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 75fffbce810acaf3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=75fffbce810acaf3 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1a23d8c795846251 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1a23d8c795846251 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3aa1b79aa6cca06b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3aa1b79aa6cca06b + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6fa88ca75caba8e4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6fa88ca75caba8e4 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 676fa9af68f6a763 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=676fa9af68f6a763 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-23' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 8b041ba8eb4cacb1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8b041ba8eb4cacb1 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-05-23' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: ac3755c1ae5f7f16 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ac3755c1ae5f7f16 + name: sra_manifest_to_concatenated_fastqs_ (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 8b4945a0fb49e03e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8b4945a0fb49e03e + name: sra_manifest_to_concatenated_fastqs_ (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 1c5a7196a442dd02 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1c5a7196a442dd02 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 7185085cbe953cd9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7185085cbe953cd9 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: e9aaa56af9d230d6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e9aaa56af9d230d6 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: eae5ae951abe6761 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=eae5ae951abe6761 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 4ba61941f31f0215 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4ba61941f31f0215 + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 7a23e64dfa6957ce + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7a23e64dfa6957ce + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 87ebf1b5956a61b5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=87ebf1b5956a61b5 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 16910402667eec78 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=16910402667eec78 + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6ecfa8ce19ed86da + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6ecfa8ce19ed86da + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fd75347cfea06651 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fd75347cfea06651 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6a174e7498434bd5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6a174e7498434bd5 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2cc5472ad7c039d1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2cc5472ad7c039d1 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1cad9a0b375ed3d1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1cad9a0b375ed3d1 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 4cc70b699ea8bc63 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4cc70b699ea8bc63 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a986e4991fc61c92 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a986e4991fc61c92 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 08da44d18689dffc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=08da44d18689dffc + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-16' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 750d086417b8a20e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=750d086417b8a20e + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-05-16' + versions: 1 +- create_time: '2024-05-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Scaffolding + - Transcriptome assembly + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 15cca0e249f40aea + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=15cca0e249f40aea + name: Ensamblaje + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - spades + - trimmomatic + - busco + update_time: '2024-05-15' + versions: 1 +- create_time: '2024-04-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: b1a98a2d5ebda1c5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5 + name: Variant Calling (DeepVariant/SNPeff) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - lofreq_call + - rseqc_bam_stat + - snpEff + - deepvariant + - bowtie2 + update_time: '2024-05-14' + versions: 0 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 2a4823c060dd216e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2a4823c060dd216e + name: sra_manifest_to_concatenated_fastqs_ (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 0775d8efad0dac10 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0775d8efad0dac10 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: b8ed069eea7879e7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b8ed069eea7879e7 + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: be46c5bb8c06a470 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=be46c5bb8c06a470 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: c5f4b7b2463f338b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c5f4b7b2463f338b + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: e817b5b275b4952f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e817b5b275b4952f + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: f7a3567ba6b57c9c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f7a3567ba6b57c9c + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 4f6e8ff94ca4f164 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4f6e8ff94ca4f164 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: deea71ccac30c7ea + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=deea71ccac30c7ea + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fcae9dfcdca70798 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fcae9dfcdca70798 + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8e509c87d143022c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8e509c87d143022c + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 52bde903adbbaf60 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=52bde903adbbaf60 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: eafe4aa62a600e1d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=eafe4aa62a600e1d + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7d11026214dd8c93 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7d11026214dd8c93 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 19c1ba21e82d8615 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=19c1ba21e82d8615 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d768a4a06d3b1a90 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d768a4a06d3b1a90 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2e029537d2f4ab50 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2e029537d2f4ab50 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-09' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 696b2efc589afd6f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=696b2efc589afd6f + name: sra_manifest_to_concatenated_fastqs_ (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: a2b4a868fa9795d1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a2b4a868fa9795d1 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 870f4988a5cc815e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=870f4988a5cc815e + name: Get Confident Peaks From ATAC or CUTandRUN replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - bedtools_bamtobed + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 9ecfaa613a112d78 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9ecfaa613a112d78 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 1388fe5d8b50bc7c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1388fe5d8b50bc7c + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 78249d353038002b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=78249d353038002b + name: Get Confident Peaks From ChIP_PE replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 962f784745c1b740 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=962f784745c1b740 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 4b92dfd20d48d479 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4b92dfd20d48d479 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 1f98df1adba71b98 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1f98df1adba71b98 + name: Get Confident Peaks From ChIP_SR replicates (release v1.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC-seq + tools: + - table_compute + - tp_text_file_with_recurring_lines + - split_file_to_collection + - collapse_dataset + - Cut1 + - bedtools_multiintersectbed + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - compose_text_param + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: de208a900880dcdc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=de208a900880dcdc + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ea61cd21e3fbad2b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ea61cd21e3fbad2b + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e0ec503626fa0d58 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e0ec503626fa0d58 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 85bc37a59a6ea443 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=85bc37a59a6ea443 + name: ATACseq (release v0.14) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c707871e1dc9e21d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c707871e1dc9e21d + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 716dc497d7d2e1c3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=716dc497d7d2e1c3 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 291829fed6fa7c44 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=291829fed6fa7c44 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-02' + versions: 1 +- create_time: '2024-05-02' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 803aec95399f7073 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=803aec95399f7073 + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-05-02' + versions: 1 +- create_time: '2023-08-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Primer removal + - Variant calling + - Sequence trimming + - DNA barcoding + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5df593510c7d944d + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5df593510c7d944d + name: DADA2 (Multiplexed reads to phyloseq tables) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - dada2_makeSequenceTable + - trimmomatic + - fastq_paired_end_joiner + - dada2_assignTaxonomyAddspecies + - __SORTLIST__ + - cutadapt + - dada2_filterAndTrim + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2024-04-27' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 4680511d4daad5d7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4680511d4daad5d7 + name: sra_manifest_to_concatenated_fastqs_ (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: e500078649dd026c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e500078649dd026c + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 8182055f5ef561f3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8182055f5ef561f3 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 79527e2b83fd5c64 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=79527e2b83fd5c64 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 5bd6d7af64192b86 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5bd6d7af64192b86 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: fda29ba2b6c98f8b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fda29ba2b6c98f8b + name: Get Confident Peaks From ChIP_SR duplicates (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9ded318097694dbc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9ded318097694dbc + name: ChIPseq_SR (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 0ebb1f5b6c9c8ab9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0ebb1f5b6c9c8ab9 + name: ATACseq (release v0.13) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 72d134a60c694b59 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=72d134a60c694b59 + name: ChIPseq_PE (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-25' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: f062eda543541ba8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f062eda543541ba8 + name: CUTandRUN (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-04-25' + versions: 1 +- create_time: '2024-04-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Sequence annotation + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 8700f593a3d642f5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8700f593a3d642f5 + name: Copy of Workflow constructed from history 'Mod 12 HW' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - stringtie + - deeptools_bam_coverage + - gffcompare + - CONVERTER_gff_to_fli_0 + - CONVERTER_gff_to_interval_index_0 + - Filter1 + - stringtie_merge + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-22' + versions: 0 +- create_time: '2024-04-18' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Data handling + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5415e85a86898e41 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=5415e85a86898e41 + name: Mega_with_custom_reference + number_of_steps: null + source: https://usegalaxy.org + tags: + - BMB554-USE-THIS + tools: + - fastp + - lofreq_alnqual + - samtools_view + - snpSift_extractFields + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - lofreq_call + - fasterq_dump + - snpEff_build_gb + - snpEff + - multiqc + - lofreq_viterbi + - bwa_mem + update_time: '2024-04-22' + versions: 4 +- create_time: '2024-04-19' + creators: [] + doi: '' + edam_operation: + - Validation + - Formatting + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: aa9def6ec8f13b3a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=aa9def6ec8f13b3a + name: Macs2 analysis + number_of_steps: null + source: https://usegalaxy.org + tags: + - BMMB582 + tools: + - multiqc + - picard_MarkDuplicates + - bedtools_multiintersectbed + - macs2_callpeak + update_time: '2024-04-19' + versions: 0 +- create_time: '2024-04-18' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 9057e2e000a7ef02 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=9057e2e000a7ef02 + name: computing_cvrg_per_strand + number_of_steps: null + source: https://usegalaxy.org + tags: + - BMMB582 + tools: + - bedtools_genomecoveragebed + - Add_a_column1 + - addValue + - collapse_dataset + update_time: '2024-04-18' + versions: 3 +- create_time: '2024-04-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 7b6ed1b7bdbe1e7f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7b6ed1b7bdbe1e7f + name: Parallel Accession Down (release v0.1.12) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-04-18' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: 69712265fdb10ed5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=69712265fdb10ed5 + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 6f1da4e0830e6051 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6f1da4e0830e6051 + name: baredSC_2d_logN (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: ebdf324634e7243c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ebdf324634e7243c + name: baredSC_1d_logN (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: c8a92318855d85a5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c8a92318855d85a5 + name: Hi-C_juicermediumtabixToCool_c (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_balance + - cooler_makebins + - cooler_cload_tabix + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: b31ab9e76409a9b7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b31ab9e76409a9b7 + name: cHi-C_fastqToCool_hicup_c (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + - compose_text_param + - Filter1 + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: f13432eef7ac28e9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f13432eef7ac28e9 + name: Hi-C_fastqToCool_hicup_c (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 4bcb4b668b9cee9e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4bcb4b668b9cee9e + name: Parallel Accession Down (release v0.1.11) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-05' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Visualisation + - Taxonomic classification + - Box-Whisker plot plotting + - Scatter plot plotting + edam_topic: [] + id: c3ea8fa3bb202dc6 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=c3ea8fa3bb202dc6 + name: UCB_Soil-Seq_ARGs_Workflow (imported from URL) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - nanoplot + - taxonomy_krona_chart + - Cut1 + - tp_replace_in_line + - join1 + - mergeCols1 + - kraken2 + - datamash_reverse + - minimap2 + update_time: '2024-04-05' + versions: 2 +- create_time: '2024-04-02' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Data handling + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0e5a3899ae97076b + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0e5a3899ae97076b + name: BMMB554_MAPPING + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastp + - samtools_view + - __FILTER_FAILED_DATASETS__ + - fasterq_dump + - multiqc + - bwa_mem + update_time: '2024-04-02' + versions: 1 +- create_time: '2024-03-31' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: bf1af666d4ea21e4 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=bf1af666d4ea21e4 + name: 'Find the exons with highest number SNPS ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2024-03-31' + versions: 0 +- create_time: '2024-03-28' + creators: + - Anna Syme + doi: '' + edam_operation: + - Visualisation + - Cross-assembly + - Mapping assembly + - Genome assembly + - De-novo assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: c8d74054c1820087 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c8d74054c1820087 + name: Genome assembly with Fly (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasta-stats + - bandage_image + - quast + - flye + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Matthias Bernt + doi: '' + edam_operation: [] + edam_topic: [] + id: 9865fee6c68fc201 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9865fee6c68fc201 + name: MetaProSIP OpenMS 2.8 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - FalseDiscoveryRate + - FeatureFinderMultiplex + - IDMapper + - MSGFPlusAdapter + - DecoyDatabase + - MetaProSIP + - __SORTLIST__ + - PeptideIndexer + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-28' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: f571e946f08c545a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f571e946f08c545a + name: Parallel Accession Down (release v0.1.10) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-03-28' + versions: 1 +- create_time: '2024-03-25' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Sequencing quality control + edam_topic: [] + id: eb3409cc73e392a8 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=eb3409cc73e392a8 + name: VSI_Data QC + number_of_steps: null + source: https://usegalaxy.org + tags: + - VeryShortIntro + tools: + - multiqc + - fastp + update_time: '2024-03-25' + versions: 1 +- create_time: '2024-03-18' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + edam_topic: [] + id: a63927dd19759714 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a63927dd19759714 + name: 'Copy of 1: Plant virus detection with kraken2 (SE) (imported from URL)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - virology + - kraken + tools: + - kraken2 + - Kraken2Tax + - taxonomy_krona_chart + update_time: '2024-03-18' + versions: 0 +- create_time: '2024-03-17' + creators: [] + doi: '' + edam_operation: + - Validation + - Formatting + - Data handling + - Sequencing quality control + edam_topic: [] + id: b11796364c22235e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b11796364c22235e + name: QC report (imported from URL) + number_of_steps: null + source: https://usegalaxy.org + tags: + - transcriptomics + tools: + - multiqc + - picard_MarkDuplicates + - rseqc_infer_experiment + - samtools_idxstats + update_time: '2024-03-18' + versions: 0 +- create_time: '2024-03-15' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Sequence analysis + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Phylogenetic tree reconstruction + edam_topic: [] + id: 9c4038fa15af6995 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=9c4038fa15af6995 + name: LBBBI29 Coffee Phylogenetic Analysis Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - newick_display + - iqtree + - rbc_mafft + update_time: '2024-03-15' + versions: 1 +- create_time: '2024-03-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8881dc79fcecf7b4 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8881dc79fcecf7b4 + name: cat this + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_tac + update_time: '2024-03-14' + versions: 0 +- create_time: '2024-03-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fa841634892b7e24 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=fa841634892b7e24 + name: Unnamed Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2024-03-14' + versions: 0 +- create_time: '2024-02-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: eb33df15225b8aa0 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=eb33df15225b8aa0 + name: 6505018-old + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gatk4_mutect2 + - samtools_sort + - trim_galore + - picard_AddOrReplaceReadGroups + - vcffilter2 + - picard_MarkDuplicates + - bwa_mem + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Matthias Bernt + - UFZ Leipzig + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: ecf3a7f9da7409ef + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ecf3a7f9da7409ef + name: dada2 amplicon analysis pipeline - for paired en (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:amplicon + tools: + - dada2_makeSequenceTable + - __UNZIP_COLLECTION__ + - dada2_seqCounts + - dada2_assignTaxonomyAddspecies + - dada2_filterAndTrim + - __APPLY_RULES__ + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 6592430b80345167 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6592430b80345167 + name: Velocyto-on10X-filtered-barcodes (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - velocyto_cli + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: e711b7a69d650590 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e711b7a69d650590 + name: Velocyto-on10X-from-bun (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - __APPLY_RULES__ + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-14' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 7c9a55db0b0eb178 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=7c9a55db0b0eb178 + name: Assembly-decontamination-VGP9 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-02-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Data handling + - Genome assembly + - Sequence alignment analysis + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: e0c33057ac2670ba + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba + name: Virus identification for pair-end data + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - kraken + - trimmomatic + - spades + - fasterq_dump + - bg_diamond + - bg_diamond_makedb + - bowtie2 + update_time: '2024-03-13' + versions: 11 +- create_time: '2024-03-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 20da2dcce0ae2ca2 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=20da2dcce0ae2ca2 + name: 'Workflow EO_BIN508_HW1 - Data 1: microbiota of a snake' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastqe + - cutadapt + update_time: '2024-03-08' + versions: 5 +- create_time: '2018-06-28' + creators: + - New England Biolabs + - Bradley W. Langhorst + - Ariel Erijman + doi: '' + edam_operation: + - Sequence file editing + - Data handling + - Nucleic acid sequence analysis + edam_topic: [] + id: 51f936d1a4e849fa + latest_version: 23 + license: AGPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=51f936d1a4e849fa + name: pRESTO NEBNext Immune Sequencing Kit Workflow v3.2.0 + number_of_steps: null + source: https://usegalaxy.org + tags: + - NEBNext + tools: + - presto_partition + - __UNZIP_COLLECTION__ + - presto_parseheaders + - presto_maskprimers + - presto_filterseq + - presto_assemblepairs + - presto_pairseq + - presto_buildconsensus + - prestor_abseq3 + - presto_collapseseq + - presto_parselog + - seqtk_sample + update_time: '2024-03-08' + versions: 23 +- create_time: '2022-01-21' + creators: + - New England Biolabs + - null + doi: '' + edam_operation: + - Sequence file editing + - Data handling + - Nucleic acid sequence analysis + edam_topic: [] + id: 34f3aac3aed0f97a + latest_version: 1 + license: AGPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=34f3aac3aed0f97a + name: pRESTO NEBNext Immune Sequencing Kit Workflow v3.2.0 + number_of_steps: null + source: https://usegalaxy.org + tags: + - NEBNext + tools: + - presto_partition + - __UNZIP_COLLECTION__ + - presto_parseheaders + - presto_maskprimers + - presto_filterseq + - presto_assemblepairs + - presto_pairseq + - presto_buildconsensus + - prestor_abseq3 + - presto_collapseseq + - presto_parselog + - seqtk_sample + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: be7dab2274c1acdd + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=be7dab2274c1acdd + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: bff8bc8d0059274f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=bff8bc8d0059274f + name: Scaffolding-BioNano-VGP7 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: fd511165e30cb62c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fd511165e30cb62c + name: baredSC_2d_logN (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 92b67534076ae889 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=92b67534076ae889 + name: baredSC_1d_logN (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 4ffdb2cf21759d26 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26 + name: 'COVID-19: consensus construction (release v0.4.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-02-27' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 334c4fe8929b5029 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=334c4fe8929b5029 + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + update_time: '2024-02-27' + versions: 0 +- create_time: '2022-10-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Mapping + - Read mapping + - Primer removal + - Sequence trimming + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a89008fccc1f1d17 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=a89008fccc1f1d17 + name: atac + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bedtools_bamtobed + - deeptools_bam_coverage + - bamFilter + - cutadapt + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + update_time: '2024-02-22' + versions: 4 +- create_time: '2024-02-22' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: 8e6d24a14d2908c2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8e6d24a14d2908c2 + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-02-22' + versions: 1 +- create_time: '2024-02-22' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 49c9e8161a46667f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=49c9e8161a46667f + name: Purge-duplicate-contigs-VGP6 (release v0.3.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-02-22' + versions: 1 +- create_time: '2024-02-15' + creators: + - Anna Syme + doi: '' + edam_operation: + - Visualisation + - Cross-assembly + - Mapping assembly + - Genome assembly + - De-novo assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 0602c14704dbe1ff + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0602c14704dbe1ff + name: Genome assembly with Fly (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasta-stats + - bandage_image + - quast + - flye + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 8ccb42012dcb5db2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=8ccb42012dcb5db2 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fcfcc7ca9ab07bce + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=fcfcc7ca9ab07bce + name: Workflow constructed from history 'SGX3 seminar' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - keras_model_config + - model_prediction + - keras_train_and_eval + - keras_model_builder + - ml_visualization_ex + update_time: '2024-02-08' + versions: 0 +- create_time: '2024-02-08' + creators: + - Kaivan Kamali + doi: '' + edam_operation: [] + edam_topic: [] + id: 8bab8e2b5d47f2f0 + latest_version: 0 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=8bab8e2b5d47f2f0 + name: Intro_To_RNN_v1_0_10_0 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - keras_model_config + - model_prediction + - keras_train_and_eval + - keras_model_builder + - ml_visualization_ex + update_time: '2024-02-08' + versions: 0 +- create_time: '2024-02-08' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 982a3eb2b4c4f5ae + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=982a3eb2b4c4f5ae + name: Mitogenome-Assembly-VGP0 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - mitohifi + - compress_file + update_time: '2024-02-08' + versions: 1 +- create_time: '2024-02-08' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: 586b923221fb5da4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=586b923221fb5da4 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-02-08' + versions: 1 +- create_time: '2024-02-08' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 31186e478383465b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=31186e478383465b + name: sra_manifest_to_concatenated_fastqs_ (release v0.2.3) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2024-02-08' + versions: 1 +- create_time: '2024-02-01' + creators: + - Gabriel + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Visualisation + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Sequencing quality control + edam_topic: [] + id: 7321c6ad5425d347 + latest_version: 1 + license: GPL-3.0-or-later + link: https://usegalaxy.org/published/workflow?id=7321c6ad5425d347 + name: Propuesta Kraken 2 - Flujo de trabajo + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - taxonomy_krona_chart + - krakentools_kreport2krona + - kraken2 + - kraken-report + - multiqc + - interactive_tool_pavian + update_time: '2024-02-01' + versions: 1 +- create_time: '2024-01-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 29d51c37d66deeeb + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=29d51c37d66deeeb + name: Velocyto-on10X-filtered-barcodes (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - velocyto_cli + update_time: '2024-01-29' + versions: 1 +- create_time: '2024-01-29' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 97ac3b8797754be8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=97ac3b8797754be8 + name: Velocyto-on10X-from-bun (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:single-cell + tools: + - __APPLY_RULES__ + update_time: '2024-01-29' + versions: 1 +- create_time: '2024-01-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b26501a4a85bfdeb + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=b26501a4a85bfdeb + name: 'WGS Project - Variant Calling and Identification of Novel Human Coronavirus ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastp + - snpSift_extractFields + - lofreq_call + - lofreq_indelqual + - fastq_dump + - samtools_stats + - snpEff + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-01-25' + versions: 5 +- create_time: '2024-01-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - De-novo assembly + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Sequence trimming + - Visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 7a33bc2d0970b502 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502 + name: Workflow constructed from history 'WGS Assessment' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - velvetg + - quast + - fastqe + - fastq_paired_end_interlacer + - cutadapt + - samtools_stats + - multiqc + - cshl_fastq_quality_filter + - bowtie2 + - velveth + update_time: '2024-01-25' + versions: 0 +- create_time: '2024-01-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4de095b92ed661ac + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4de095b92ed661ac + name: 'Whole genome sequencing project for discovering novel coronavirus from 2 + pneumonia cases ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastp + - snpSift_extractFields + - lofreq_call + - lofreq_indelqual + - fastq_dump + - samtools_stats + - snpEff + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-01-25' + versions: 0 +- create_time: '2024-01-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Visualisation + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 582f3de3971fc38c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=582f3de3971fc38c + name: RNA-Seq and Metatranscriptomics project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gtftobed12 + - tp_sort_header_tool + - fasterq_dump + - pygenomeTracks + - cutadapt + - __FLATTEN__ + - rseqc_infer_experiment + - rna_star + - multiqc + - featurecounts + update_time: '2024-01-25' + versions: 0 +- create_time: '2024-01-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Visualisation + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e33f6a058c5f57e5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5 + name: Workflow for SRR16039774 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gtftobed12 + - tp_sort_header_tool + - pygenomeTracks + - fastq_dump + - cutadapt + - __FLATTEN__ + - rseqc_infer_experiment + - rna_star + - multiqc + - featurecounts + update_time: '2024-01-25' + versions: 0 +- create_time: '2024-01-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - SNP detection + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 62436fe121e035e7 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=62436fe121e035e7 + name: BIOL3019 CAII WGS - SARS-CoV-2 Variant Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - snpSift_extractFields + - lofreq_call + - lofreq_indelqual + - cutadapt + - jbrowse + - samtools_stats + - snpeff_sars_cov_2 + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-01-24' + versions: 1 +- create_time: '2024-01-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5b2bb861501fa248 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5b2bb861501fa248 + name: BIOL3019 CAII SARS-CoV-2 Variant Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + - jbrowse + - bwa_mem + update_time: '2024-01-24' + versions: 1 +- create_time: '2024-01-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: efa598aa9b7cb0b1 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=efa598aa9b7cb0b1 + name: GASPhipseq setA - fastQ to Mapped reads with QC + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - qualimap_bamqc + - bowtie2 + - featurecounts + update_time: '2024-01-23' + versions: 1 +- create_time: '2024-01-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e7586d70715207b5 + latest_version: 38 + license: null + link: https://usegalaxy.org/published/workflow?id=e7586d70715207b5 + name: rnaseq_test + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - deepvariant + - vcftools_annotate + - cutadapt + - __FLATTEN__ + - snpEff + - multiqc + - picard_MarkDuplicates + - bowtie2 + update_time: '2024-01-22' + versions: 38 +- create_time: '2024-01-18' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: d3f35215e6f45d79 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=d3f35215e6f45d79 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 31a6145b0832fa48 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=31a6145b0832fa48 + name: Assembly-Hifi-only-VGP3 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 8b81b9a3b49bbf98 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98 + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 786aa9e2bd723629 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=786aa9e2bd723629 + name: 'COVID-19: variation analysis on WGS SE (release v0.1.4)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: ba347b695dbff2ea + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=ba347b695dbff2ea + name: Workflow of practical history + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - bcftools_norm + - snpEff + - samtools_view + - multiqc + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 1 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Generation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ff35347c4e2f0e81 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ff35347c4e2f0e81 + name: Workflow constructed from history 'Complete Workflow Exam' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - samtools_view + - multiqc + - bwa_mem + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 496b0e8a0e5a4191 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=496b0e8a0e5a4191 + name: Hana AlDaoud_1120871536 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - snpEff + - samtools_view + - multiqc + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4375f00f8a285088 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=4375f00f8a285088 + name: From Peaks to Gene + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_intersect_1 + update_time: '2024-01-13' + versions: 1 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: cd4b5b62f1eed51b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=cd4b5b62f1eed51b + name: exam + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_view + - samtools_rmdup + - multiqc + - bowtie2 + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c75fcf2b7ba057fd + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c75fcf2b7ba057fd + name: Eyad_Alqaysi_1118537255 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gemini_load + - samtools_rmdup + - bcftools_norm + - snpEff + - samtools_view + - multiqc + - freebayes + - bwa_mem + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: d5062ef48aa246d8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d5062ef48aa246d8 + name: EyadAlqaysi_1118537255 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - samtools_view + - multiqc + - bowtie2 + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 76fff93650152579 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=76fff93650152579 + name: Workflow constructed from history 'the test maram alrazhi' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - multiqc + - bowtie2 + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 371b242d97f2f030 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=371b242d97f2f030 + name: Workflow constructed from history 'Nada Ali Alzahrani - exam' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - bcftools_norm + - snpEff + - samtools_view + - multiqc + - freebayes + - bwa_mem + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 70dacee3da375e2b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=70dacee3da375e2b + name: Workflow constructed from history 'identify and analyze genetic mutations, + incorporating necessary quality control measures' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - vcfallelicprimitives + - samtools_stats + - snpEff + - multiqc + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: f2d3abc6c45c4839 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f2d3abc6c45c4839 + name: Workflow constructed from history 'Human Whole-Exome Sequences for three individuals. + Sequenced' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - samtools_view + - multiqc + - bowtie2 + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 9bf1d223a57f88da + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=9bf1d223a57f88da + name: 'Workflow constructed from history ''Exam: Human Whole-Exome Sequences for + three individuals. Sequenced''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - samtools_view + - multiqc + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 1b57987895f8ca9e + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=1b57987895f8ca9e + name: Workflow constructed from history 'Exam Norah' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - snpEff + - samtools_view + - multiqc + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 1 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: d3704f2927e3065e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d3704f2927e3065e + name: Workflow constructed from history 'Exam - Aljouhra AlHargan' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - multiqc + - samtools_stats + - bowtie2 + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Sequence composition calculation + - Read mapping + - Primer removal + - Variant calling + - Sequence trimming + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 49c61c378cacfe02 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=49c61c378cacfe02 + name: Workflow constructed from history 'part2' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + - jbrowse + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 1 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e64a6119053cb126 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e64a6119053cb126 + name: Workflow constructed from history 'Identify and analyze genetic mutations' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - samtools_view + - multiqc + - freebayes + - bwa_mem + update_time: '2024-01-13' + versions: 1 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 08f58af7b6cc0ab6 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=08f58af7b6cc0ab6 + name: '''Genetic Mutation by Manar Alzanbaqi''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - bcftools_norm + - snpEff + - samtools_view + - multiqc + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 1 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 0e6a842034ca9aec + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0e6a842034ca9aec + name: '''Amal Magbel Alotaibi_1082516236''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - multiqc + - bowtie2 + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: a0451d7084d7732b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a0451d7084d7732b + name: Workflow constructed from history 'EXAM' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - snpEff + - samtools_view + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 48963532e030de6c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=48963532e030de6c + name: work flow 'Exam practical(Eman Taha 2407042999)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_rmdup + - bcftools_norm + - snpEff + - samtools_view + - multiqc + - bowtie2 + - freebayes + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c2b299627d2baf48 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c2b299627d2baf48 + name: Workflow constructed from history 'Peaks to genes' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - get_flanks1 + - tp_sort_header_tool + - CONVERTER_interval_to_bed_0 + - gops_intersect_1 + - Grouping1 + - tp_tail_tool + - tp_replace_in_column + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0558fabfff88ee59 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0558fabfff88ee59 + name: Workflow constructed from history 'variant mapping by sequence' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - mimodd_vcf_filter + - mimodd_varcall + - mimodd_map + - snpEff + - snpEff_download + - mimodd_varreport + - mimodd_varextract + update_time: '2024-01-13' + versions: 0 +- create_time: '2024-01-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b6d90898e2db6aba + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b6d90898e2db6aba + name: Workflow constructed from history 'Assessment pipeline for snpeff/sift' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2024-01-10' + versions: 0 +- create_time: '2024-01-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2497103d279cd20e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=2497103d279cd20e + name: Workflow constructed from history 'Alternative Filtering' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2024-01-10' + versions: 0 +- create_time: '2024-01-10' + creators: [] + doi: '' + edam_operation: + - 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Validation + - Sequence analysis + - Phylogenetic tree analysis + - Gene prediction + - Sequencing quality control + edam_topic: [] + id: d4f0a7ccb09f1e55 + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55 + name: PDAMR + number_of_steps: null + source: https://usegalaxy.org + tags: + - WGS + - Illumina + - pathogen + - workflow + tools: + - fastp + - Kraken2Tax + - snippy + - staramr_search + - merqury + - shovill + - prokka + - kraken2 + - snippy_core + - snp_dists + - multiqc + - raxml + update_time: '2023-12-13' + versions: 10 +- create_time: '2023-12-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Visualisation + - Data handling + - Taxonomic classification + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 5b74b780d3955eb3 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5b74b780d3955eb3 + name: Workflow constructed from history 'SRA-paired-end' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_dump + - taxonomy_krona_chart + - kraken2 + update_time: '2023-12-08' + versions: 0 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 1a08efa0bf83d225 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1a08efa0bf83d225 + name: baredSC_2d_logN (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: ff84d87fd3638a3f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ff84d87fd3638a3f + name: baredSC_1d_logN (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 3d7a9694bcee6db5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3d7a9694bcee6db5 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: d6cf3be79a4b7db4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d6cf3be79a4b7db4 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 68b995393b3142ec + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=68b995393b3142ec + name: Get Confident Peaks From ChIP_SR duplicates (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-11-09' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: 030814e5329ea62d + latest_version: 24 + license: null + link: https://usegalaxy.org/published/workflow?id=030814e5329ea62d + name: DESeq2 Workflow_Daxton + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - __BUILD_LIST__ + - deseq2 + - __TAG_FROM_FILE__ + update_time: '2023-12-07' + versions: 24 +- create_time: '2023-12-04' + creators: [] + doi: '' + edam_operation: + - Scaffolding + - Genome annotation + - Genome visualisation + - Transcriptome assembly + - Genome assembly + - Sequence assembly validation + - Sequence annotation + edam_topic: [] + id: dbe08700353dfc43 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=dbe08700353dfc43 + name: Workflow constructed from history 'Genome annotation' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gffread + - jcvi_gff_stats + - fasta-stats + - maker_map_ids + - jbrowse + - maker + - busco + update_time: '2023-12-04' + versions: 3 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: f7d1c6be4e4c3357 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f7d1c6be4e4c3357 + name: Generic variation analysis reporting (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - mpvx + - generic + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - compose_text_param + - tp_find_and_replace + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: ea206593698adbfd + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=ea206593698adbfd + name: Assembly-decontamination-VGP9 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 3db4eb1ecb588d44 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=3db4eb1ecb588d44 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: 4a0ad87aa5aa558a + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=4a0ad87aa5aa558a + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: c72f94a30ad54327 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=c72f94a30ad54327 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 815cd221eaaaeb53 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=815cd221eaaaeb53 + name: kmer-profiling-hifi-VGP1 (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: eaf96fa3c39c210b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=eaf96fa3c39c210b + name: Purge-duplicate-contigs-VGP6 (release v0.3.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 9f4c4038d1c519e2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2 + name: Scaffolding-HiC-VGP8 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 46207bf9ce5ee26a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=46207bf9ce5ee26a + name: sra_manifest_to_concatenated_fastqs_ (release v0.2.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 2b41752b8518a87b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=2b41752b8518a87b + name: Assembly-Hifi-only-VGP3 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 5aa4b9131c31cb79 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5aa4b9131c31cb79 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 8cf06b14037a8d5a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8cf06b14037a8d5a + name: Get Confident Peaks From ChIP_PE duplicates (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 438761debd08a9be + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=438761debd08a9be + name: Get Confident Peaks From ChIP_SR duplicates (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 326ced2230a49c26 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=326ced2230a49c26 + name: CUTandRUN (release v0.6.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 34ab5572a9547bfe + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=34ab5572a9547bfe + name: Generic variation analysis on WGS PE (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - mpxv + - generic + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: a638e12411586555 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a638e12411586555 + name: Create GRO and TOP complex files (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - ambertools_acpype + - Cut1 + - ctb_rdkit_descriptors + - gmx_setup + - tp_grep_tool + - gmx_merge_topology_files + - param_value_from_file + - ambertools_antechamber + - openbabel_compound_convert + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: ad19db6504b6dc33 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33 + name: MMGBSA calculations with GROMACS (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 442a2868873e7f77 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=442a2868873e7f77 + name: MMGBSA calculations with GROMACS (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 28c7e8269d478244 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=28c7e8269d478244 + name: dcTMD calculations with GROMACS (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_text_file_with_recurring_lines + - split_file_to_collection + - add_line_to_file + - tp_cat + - gmx_sim + - biomd_neqgamma + - gmx_solvate + - tp_sed_tool + - gmx_makendx + - compose_text_param + - ctb_online_data_fetch + - param_value_from_file + - gmx_em + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 23be272392a4b83b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=23be272392a4b83b + name: Parallel Accession Down (release v0.1.9) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 7b20a62d69d53efc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc + name: 'COVID-19: consensus construction (release v0.4.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 8a01c78688beae1d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8a01c78688beae1d + name: 'COVID-19: variation analysis reporting (release v0.3.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 15a0e22570f71098 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=15a0e22570f71098 + name: 'COVID-19: variation analysis on WGS PE (release v0.2.4)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4f459cfef6108e75 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4f459cfef6108e75 + name: Alignment_Variant_Calling_and_Filtering-v0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-11-28' + versions: 0 +- create_time: '2023-11-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: bfbfbf7e08bc3615 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=bfbfbf7e08bc3615 + name: Alignment_Variant_Calling_and_Filtering-v0.1 - EP + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2023-11-27' + versions: 0 +- create_time: '2023-11-23' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: cff93a6f24af5fee + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=cff93a6f24af5fee + name: Deseq2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - __TAG_FROM_FILE__ + - deseq2 + update_time: '2023-11-24' + versions: 1 +- create_time: '2023-11-24' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: c8ee2da45b6889b9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c8ee2da45b6889b9 + name: Copy of Deseq2 shared by user omkar12345 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - __TAG_FROM_FILE__ + - deseq2 + update_time: '2023-11-24' + versions: 0 +- create_time: '2023-11-23' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 27144c7e44d3f56b + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=27144c7e44d3f56b + name: Basics + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - deg_annotate + - trimmomatic + - stringtie + - deseq2 + - hisat2 + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 605160c81d098703 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=605160c81d098703 + name: Assembly-decontamination-VGP9 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 7f6900852a81d121 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=7f6900852a81d121 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 9bc46b4d35749b41 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=9bc46b4d35749b41 + name: kmer-profiling-hifi-VGP1 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 3753dcca4100e976 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=3753dcca4100e976 + name: Purge-duplicate-contigs-VGP6 (release v0.3.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: c09b8a0c96123cbb + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=c09b8a0c96123cbb + name: Purge-duplicate-contigs-VGP6 (release v0.3.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 155839aeb6340f54 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=155839aeb6340f54 + name: Scaffolding-HiC-VGP8 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 28ddea356ae57da1 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=28ddea356ae57da1 + name: Scaffolding-HiC-VGP8 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 3511da8b41b1fb5d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3511da8b41b1fb5d + name: sra_manifest_to_concatenated_fastqs_ (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Lucille Delisle + - Pierre Osteil + - Wolfgang Maier + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: c7693951c6215e19 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c7693951c6215e19 + name: sra_manifest_to_concatenated_fastqs_ (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - map_param_value + - split_file_to_collection + - Cut1 + - fasterq_dump + - __RELABEL_FROM_FILE__ + - compose_text_param + - tp_find_and_replace + - __APPLY_RULES__ + - cat_multi_datasets + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 01193a261e246899 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=01193a261e246899 + name: Parallel Accession Down (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 9f38a8d3e373d05c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9f38a8d3e373d05c + name: Parallel Accession Down (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5cb86cdc33296cc2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5cb86cdc33296cc2 + name: Workflow constructed from history 'RUNASEQ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cufflinks + - samtools_sort + - cuffdiff + - fastq_dump + - hisat2 + update_time: '2023-11-20' + versions: 0 +- create_time: '2023-11-18' + creators: [] + doi: '' + edam_operation: + - Sequence assembly visualisation + - Genome assembly + edam_topic: [] + id: 8a350e0d96e937a5 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=8a350e0d96e937a5 + name: Novo Assembly + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bandage_image + - spades + - bandage_info + update_time: '2023-11-19' + versions: 2 +- create_time: '2023-11-16' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: e887adf3afc3253d + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=e887adf3afc3253d + name: Assembly-decontamination-VGP9 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 85f521f5c7351406 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=85f521f5c7351406 + name: Scaffolding-BioNano-VGP7 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: b7b69aaee5202144 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b7b69aaee5202144 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: f58aa85ceaa19534 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f58aa85ceaa19534 + name: Get Confident Peaks From ChIP_PE duplicates (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 5b540de61a70df64 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5b540de61a70df64 + name: Get Confident Peaks From ChIP_SR duplicates (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-08' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: eb01b539d17580c3 + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=eb01b539d17580c3 + name: Differential Gene Expression Analysis - Untreated | Condition 1 | Condition + 2 into DESeq2 + number_of_steps: null + source: https://usegalaxy.org + tags: + - DESeq2 + - Differential + - FastQC + - HISAT2 + - RNAseq + - expression + - featureCounts + - multiple + tools: + - fastqc + - trimmomatic + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-11-13' + versions: 9 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 19e2191687f81c21 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=19e2191687f81c21 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 7f8d7595cbeebf1d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=7f8d7595cbeebf1d + name: kmer-profiling-hifi-VGP1 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 634bbef1f67a0e30 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30 + name: dcTMD calculations with GROMACS (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_text_file_with_recurring_lines + - split_file_to_collection + - add_line_to_file + - tp_cat + - gmx_sim + - biomd_neqgamma + - gmx_solvate + - tp_sed_tool + - gmx_makendx + - compose_text_param + - ctb_online_data_fetch + - param_value_from_file + - gmx_em + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: bcce65725298ff33 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=bcce65725298ff33 + name: QC_HW + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + update_time: '2023-11-13' + versions: 4 +- create_time: '2023-11-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 2e4918ad409f7f4e + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2e4918ad409f7f4e + name: Quality check Reads - cutadapt + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + update_time: '2023-11-12' + versions: 1 +- create_time: '2023-11-10' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Visualisation + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Sequencing quality control + edam_topic: [] + id: 60f0d0d5d6e93941 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=60f0d0d5d6e93941 + name: Workflow constructed from history 'Beer-oxford nanopore' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastp + - taxonomy_krona_chart + - krakentools_kreport2krona + - kraken2 + - porechop + - Filter1 + update_time: '2023-11-10' + versions: 0 +- create_time: '2023-11-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ddbf7b0321582f23 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ddbf7b0321582f23 + name: Beer-oxford nanopore + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2023-11-10' + versions: 0 +- create_time: '2023-11-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 886d825f217542e1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=886d825f217542e1 + name: test_2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2023-11-09' + versions: 0 +- create_time: '2023-11-09' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: cace9f1359874352 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org/published/workflow?id=cace9f1359874352 + name: Assembly-decontamination-VGP9 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 683e725f672b7d9b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=683e725f672b7d9b + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: e4dd39237df58884 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=e4dd39237df58884 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fc7b14aafa0b421e + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=fc7b14aafa0b421e + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: b661fb850c4b4b01 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=b661fb850c4b4b01 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: dae5d5e5df5c4dd7 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=dae5d5e5df5c4dd7 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: ca3f2d9554e9e1c8 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=ca3f2d9554e9e1c8 + name: Scaffolding-BioNano-VGP7 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: bcf3ff03326c80b7 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=bcf3ff03326c80b7 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: faa4f94f070c6213 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=faa4f94f070c6213 + name: kmer-profiling-hifi-VGP1 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: ae71399852f34680 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=ae71399852f34680 + name: kmer-profiling-hifi-VGP1 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 5edabfc62f58d8cf + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=5edabfc62f58d8cf + name: Purge-duplicate-contigs-VGP6 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: d2e8a6b39fe88f4c + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=d2e8a6b39fe88f4c + name: Purge duplicate contigs (WF6 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 45c0b677c4920d03 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=45c0b677c4920d03 + name: Purge duplicate contigs (WF6 (release v0.2.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 96bd0007dceec123 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=96bd0007dceec123 + name: Purge-duplicate-contigs-VGP6 (release v0.3.0) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 903e35b62946ed76 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=903e35b62946ed76 + name: Scaffolding-HiC-VGP8 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 88327cb2e0fe3c25 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25 + name: Scaffolding-HiC-VGP8 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 6cad14c78ec330ac + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6cad14c78ec330ac + name: baredSC_2d_logN (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 3d0f92e7f63978b6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3d0f92e7f63978b6 + name: baredSC_1d_logN (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3c0af11dbeeee506 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3c0af11dbeeee506 + name: ChIPseq_SR (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fcbe12fc4eaae12e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=fcbe12fc4eaae12e + name: ATACseq (release v0.7) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e899acc664c8b808 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e899acc664c8b808 + name: ATACseq (release v0.8) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: de29cd965a2e93d3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=de29cd965a2e93d3 + name: ATACseq (release v0.9) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 69edab5d6ad91556 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=69edab5d6ad91556 + name: ChIPseq_PE (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 52b7524a3941885c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=52b7524a3941885c + name: CUTandRUN (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-09' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5a16ff38eb80da82 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5a16ff38eb80da82 + name: CUTandRUN (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-09' + versions: 1 +- create_time: '2023-11-08' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Visualisation + - Taxonomic classification + - Scatter plot plotting + - Box-Whisker plot plotting + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 21161075002d6778 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=21161075002d6778 + name: Case study 4 williams + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - nanoplot + - fastp + - taxonomy_krona_chart + - kraken2 + - porechop + update_time: '2023-11-08' + versions: 0 +- create_time: '2023-11-08' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Visualisation + - Taxonomic classification + - Scatter plot plotting + - Box-Whisker plot plotting + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: b7817a12dbee583c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b7817a12dbee583c + name: Copy of Case study 4 williams + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - nanoplot + - fastp + - taxonomy_krona_chart + - kraken2 + - porechop + update_time: '2023-11-08' + versions: 0 +- create_time: '2023-08-31' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: 6f090b2c259847d2 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=6f090b2c259847d2 + name: Finalized Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: + - metagenomics + tools: + - mothur_heatmap_sim + - mothur_rarefaction_single + - mothur_align_seqs + - mothur_classify_seqs + - mothur_venn + - taxonomy_krona_chart + - mothur_make_shared + - newick_display + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_dist_shared + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_tree_shared + - mothur_unique_seqs + - mothur_classify_otu + - mothur_taxonomy_to_krona + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - XY_Plot_1 + - mothur_count_groups + - mothur_cluster_split + - mothur_sub_sample + - mothur_pre_cluster + update_time: '2023-11-06' + versions: 6 +- create_time: '2023-11-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 26019c2b056d3a1c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=26019c2b056d3a1c + name: Workflow constructed from history 'RNA-Seq2' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + - __FLATTEN__ + - rna_star + - multiqc + update_time: '2023-11-06' + versions: 0 +- create_time: '2023-11-06' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: 19fcce20ecaf2ef6 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=19fcce20ecaf2ef6 + name: Workflow constructed from history 'Fruit Fly' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deg_annotate + - collection_element_identifiers + - Cut1 + - tp_replace_in_line + - join1 + - ggplot2_heatmap2 + - cat1 + - __TAG_FROM_FILE__ + - deseq2 + - Filter1 + update_time: '2023-11-06' + versions: 0 +- create_time: '2023-11-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: a89d1b74566d516d + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a89d1b74566d516d + name: Workflow constructed from history 'QC' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + update_time: '2023-11-06' + versions: 1 +- create_time: '2023-11-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7497bfdd2085b6e0 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=7497bfdd2085b6e0 + name: Workflow constructed from history 'Visualization of RNA-Seq results with Volcano + Plot' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - volcanoplot + update_time: '2023-11-05' + versions: 0 +- create_time: '2023-11-04' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + - Read summarisation + - Sequence annotation + - RNA-Seq quantification + edam_topic: [] + id: 2a7fbfc1c17e38bc + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=2a7fbfc1c17e38bc + name: FloraBERT (Trimmomatic + HISAT2 + featureCounts) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gffread + - trimmomatic + - featurecounts + - hisat2 + update_time: '2023-11-04' + versions: 2 +- create_time: '2023-11-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - De-novo assembly + - Sequence composition calculation + - Validation + - Visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 4e1ae78405034ad3 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3 + name: Workflow constructed from history 'Genome Assembly' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - velvetg + - quast + - fastq_paired_end_interlacer + - multiqc + - velveth + update_time: '2023-11-04' + versions: 6 +- create_time: '2023-11-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: dc7f05cb5a62da77 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=dc7f05cb5a62da77 + name: Workflow constructed from history 'Mapping' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + - __FLATTEN__ + - rna_star + - multiqc + update_time: '2023-11-03' + versions: 0 +- create_time: '2023-11-03' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: abf1aec0f3d48d03 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=abf1aec0f3d48d03 + name: Workflow constructed from history 'DEG' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deg_annotate + - table_compute + - collection_element_identifiers + - Cut1 + - tp_replace_in_line + - tp_cat + - join1 + - ggplot2_heatmap2 + - __TAG_FROM_FILE__ + - deseq2 + - Filter1 + update_time: '2023-11-03' + versions: 0 +- create_time: '2023-10-31' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 27e174711b459ddf + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=27e174711b459ddf + name: Workflow constructed from history '202360-50597870-Galaxy101' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bedtools_intersectbed + - datamash_ops + update_time: '2023-10-31' + versions: 0 +- create_time: '2023-10-31' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: b3d83022d4944404 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b3d83022d4944404 + name: Workflow constructed from history '202360-50597870-Galaxy101' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bedtools_intersectbed + - datamash_ops + update_time: '2023-10-31' + versions: 0 +- create_time: '2023-10-26' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 283bc048cc7a80f5 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=283bc048cc7a80f5 + name: Assembly-Hifi-only-VGP3 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2023-10-26' + versions: 1 +- create_time: '2021-02-17' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - Sequence composition calculation + - Read mapping + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: dcc7c5fdef8780fd + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=dcc7c5fdef8780fd + name: RNA-seq Data Processing + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - deg_annotate + - Cut1 + - tp_sort_header_tool + - collapse_dataset + - join1 + - ggplot2_heatmap2 + - cat1 + - tp_cut_tool + - htseq_count + - fastq_groomer + - bowtie2 + - deseq2 + - Filter1 + update_time: '2023-10-24' + versions: 8 +- create_time: '2023-10-19' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + - Phylogenetic tree generation (from molecular sequences) + edam_topic: [] + id: 3d7baebefa7c9b81 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81 + name: Workflow 'Armado de AF automatizado' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasttree + - clustalw + update_time: '2023-10-19' + versions: 1 +- create_time: '2023-10-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0052e9b1b7bfec69 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0052e9b1b7bfec69 + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cufflinks + - samtools_sort + - cuffdiff + - fastq_dump + - hisat2 + update_time: '2023-10-19' + versions: 0 +- create_time: '2023-10-11' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 0f6bb7847f8769af + latest_version: 5 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0f6bb7847f8769af + name: baredSC_2d_logNorm + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2023-10-19' + versions: 5 +- create_time: '2023-10-17' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 0bb15b58857c12b8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0bb15b58857c12b8 + name: Hmwk 7-8 MWL Q1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bedtools_intersectbed + update_time: '2023-10-17' + versions: 0 +- create_time: '2023-10-12' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: b3f2647ad8eeb620 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=b3f2647ad8eeb620 + name: Simons Vetting (101223) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bedtools_subtractbed + - bedtools_intersectbed + update_time: '2023-10-12' + versions: 2 +- create_time: '2023-10-06' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + - Phylogenetic tree generation (from molecular sequences) + edam_topic: [] + id: 87685c6247521b54 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=87685c6247521b54 + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasttree + - clustalw + update_time: '2023-10-06' + versions: 0 +- create_time: '2023-10-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 36a32a845cdeb93e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=36a32a845cdeb93e + name: Average Bigwig between replicates (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deeptools_bigwig_average + - __APPLY_RULES__ + update_time: '2023-10-05' + versions: 1 +- create_time: '2023-10-05' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b63d1e1024cc3295 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b63d1e1024cc3295 + name: ATACseq (release v0.6) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-10-05' + versions: 1 +- create_time: '2023-10-05' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 278c8f376de66bd7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=278c8f376de66bd7 + name: Parallel Accession Down (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-10-05' + versions: 1 +- create_time: '2023-10-01' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + edam_topic: [] + id: cf3f0760611f22f9 + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=cf3f0760611f22f9 + name: 'FloraBERT Test (Trimmomatic + HISAT2 + featureCounts) ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - featurecounts + - hisat2 + update_time: '2023-10-04' + versions: 13 +- create_time: '2023-08-31' + creators: [] + doi: '' + edam_operation: + - Validation + - Formatting + - Data handling + - Sequencing quality control + edam_topic: [] + id: 7e9269e78e989480 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=7e9269e78e989480 + name: QC report (imported from URL) + number_of_steps: null + source: https://usegalaxy.org + tags: + - transcriptomics + tools: + - multiqc + - picard_MarkDuplicates + - rseqc_infer_experiment + - samtools_idxstats + update_time: '2023-10-02' + versions: 0 +- create_time: '2023-09-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 8bd051791178953a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8bd051791178953a + name: Average Bigwig between replicates (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deeptools_bigwig_average + - __APPLY_RULES__ + update_time: '2023-09-28' + versions: 1 +- create_time: '2023-09-28' + creators: + - Romane Libouban + doi: '' + edam_operation: + - Genome annotation + - Repeat sequence detection + edam_topic: [] + id: effc17e170263ae6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=effc17e170263ae6 + name: Repeat masking with RepeatModeler and RepeatMask (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - repeatmasker_wrapper + - repeatmodeler + update_time: '2023-09-28' + versions: 1 +- create_time: '2023-09-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8a215695e7b57cf5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=8a215695e7b57cf5 + name: ATACseq (release v0.5.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - __APPLY_RULES__ + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-09-28' + versions: 1 +- create_time: '2023-09-26' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Formatting + - Data handling + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 98286b6154e1b57f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=98286b6154e1b57f + name: Workflow constructed from history '#2 AA' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - CONVERTER_gz_to_uncompressed + - fastp + - picard_NormalizeFasta + - cshl_fastx_collapser + - fastq_dump + - rbc_mirdeep2_quantifier + - rbc_mirdeep2 + - rbc_mirdeep2_mapper + update_time: '2023-09-26' + versions: 0 +- create_time: '2023-09-23' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + edam_topic: [] + id: b06c96cb684e30a4 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=b06c96cb684e30a4 + name: MSA-pipeline + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - clustalw + update_time: '2023-09-23' + versions: 1 +- create_time: '2023-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: a00f78b74c27b5f3 + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=a00f78b74c27b5f3 + name: K-mer profiling and QC (WF1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - VGP + - BGA23 + tools: + - meryl + - genomescope + update_time: '2023-09-21' + versions: 2 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 2ffae50d0916b641 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2ffae50d0916b641 + name: Hi-C_fastqToPairs_hic (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - hicup2juicer + - compose_text_param + - hicup_hicup + - Filter1 + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 53fdff74729a6780 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=53fdff74729a6780 + name: RNAseq_PE (release v0.4.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 2f774500d5bec9a6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2f774500d5bec9a6 + name: RNAseq_PE (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3e6c9ab5ef3250ae + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3e6c9ab5ef3250ae + name: RNAseq_SR (release v0.4.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-09-21' + versions: 1 +- create_time: '2023-09-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 63b3b266bde77563 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=63b3b266bde77563 + name: RNAseq_SR (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2023-09-21' + versions: 1 +- create_time: '2021-06-21' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: dd43ae9a5b303086 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=dd43ae9a5b303086 + name: Filter, Plot and Explore Single-cell RNA-seq Data (imported from uploaded + file) + number_of_steps: null + source: https://usegalaxy.org + tags: + - transcriptomics + - name:singlecell + tools: + - anndata_manipulate + - scanpy_find_cluster + - scanpy_scale_data + - anndata_inspect + - scanpy_compute_graph + - scanpy_find_markers + - scanpy_plot_embed + - Cut1 + - scanpy_normalise_data + - join1 + - scanpy_run_tsne + - scanpy_filter_cells + - scanpy_filter_genes + - scanpy_run_umap + - scanpy_plot + - anndata_ops + - scanpy_find_variable_genes + - scanpy_run_pca + update_time: '2023-09-20' + versions: 1 +- create_time: '2023-09-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 802f5ff14a924e42 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=802f5ff14a924e42 + name: scRNAseq ESIS + number_of_steps: null + source: https://usegalaxy.org + tags: + - scESIS + tools: + - scanpy_find_variable_genes + - scanpy_filter_cells + update_time: '2023-09-14' + versions: 5 +- create_time: '2023-09-13' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Data handling + - Sequence alignment analysis + - RNA-Seq quantification + - Sequence alignment + - Read summarisation + edam_topic: [] + id: dab54002b3c0e351 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=dab54002b3c0e351 + name: ncRNA analysis single-end v 4.0 + number_of_steps: null + source: https://usegalaxy.org + tags: + - CPB + tools: + - collection_column_join + - bamFilter + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-09-14' + versions: 5 +- create_time: '2023-09-14' + creators: + - Anna Syme + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Mapping assembly + edam_topic: [] + id: bcdc5ce2ea8700fc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bcdc5ce2ea8700fc + name: Assembly polishing with long reads (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - minimap2 + - racon + update_time: '2023-09-14' + versions: 1 +- create_time: '2023-09-14' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: bcd23aee681e5af5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bcd23aee681e5af5 + name: Parallel Accession Down (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-09-14' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 23468eea382e6bb4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=23468eea382e6bb4 + name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - random_lines1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - wc_gnu + - macs2_callpeak + - multiqc + - wig_to_bigWig + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 6dcb43f86b9cd7dc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6dcb43f86b9cd7dc + name: Get Confident Peaks From ChIP_PE duplicates (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - Peak calling + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 6a2dace98986992a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6a2dace98986992a + name: Get Confident Peaks From ChIP_SR duplicates (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - table_compute + - __EXTRACT_DATASET__ + - collapse_dataset + - Cut1 + - param_value_from_file + - bedtools_intersectbed + - deeptools_bigwig_average + - tp_sorted_uniq + - macs2_callpeak + - samtools_view + - wig_to_bigWig + - multiqc + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: a93eb877596ce0ef + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=a93eb877596ce0ef + name: Hi-C_juicermediumtabixToCool_c (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_balance + - cooler_makebins + - cooler_cload_tabix + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 748c1a9d85eb61e2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=748c1a9d85eb61e2 + name: Hi-C_fastqToPairs_hic (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - hicup2juicer + - compose_text_param + - hicup_hicup + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 1e4eb6ccb47d9fc7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1e4eb6ccb47d9fc7 + name: Hi-C_juicermediumtabixToCool_c (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_balance + - cooler_makebins + - cooler_cload_tabix + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: f80b80aa7fb196ba + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f80b80aa7fb196ba + name: cHi-C_fastqToCool_hicup_c (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + - compose_text_param + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 0bc1b8888d8b20c4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0bc1b8888d8b20c4 + name: Hi-C_fastqToCool_hicup_c (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: ba4815ec62edab04 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ba4815ec62edab04 + name: Hi-C_fastqToPairs_hic (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - hicup2juicer + - compose_text_param + - hicup_hicup + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 7353afb9301780e5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7353afb9301780e5 + name: cHi-C_fastqToCool_hicup_c (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + - compose_text_param + - Filter1 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 4998f171ec922c7d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4998f171ec922c7d + name: Hi-C_fastqToCool_hicup_c (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 90ed607bedd65524 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=90ed607bedd65524 + name: ChIPseq_SR (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b5e8f4a0ff226921 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=b5e8f4a0ff226921 + name: ATACseq (release v0.5) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - deeptools_bigwig_average + - picard_MarkDuplicates + - bowtie2 + - pe_histogram + - samtools_idxstats + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - multiqc + - bedtools_mergebed + - Add_a_column1 + - tp_awk_tool + - bedtools_slopbed + - macs2_callpeak + - param_value_from_file + - bamFilter + - bedtools_coveragebed + - samtools_view + - wig_to_bigWig + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: cb011900fc0ee12a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=cb011900fc0ee12a + name: ChIPseq_PE (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 67992bf894a82587 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=67992bf894a82587 + name: CUTandRUN (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 4dfe253e26b29052 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4dfe253e26b29052 + name: Parallel Accession Down (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-08-12' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: fca70e1bf761c6a2 + latest_version: 22 + license: null + link: https://usegalaxy.org/published/workflow?id=fca70e1bf761c6a2 + name: 'Trim seq 18S ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sickle + update_time: '2023-09-02' + versions: 22 +- create_time: '2023-08-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: efb10012b8448b21 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=efb10012b8448b21 + name: RNA-seq (Sue-ob, K.) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - samtools_sort + - samtools_stats + - htseq_count + - samtool_filter2 + - hisat2 + update_time: '2023-08-29' + versions: 1 +- create_time: '2023-07-19' + creators: + - Wendi Bacon + - Julia Jakiela + doi: '' + edam_operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + edam_topic: [] + id: a2a924b871b1c96d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d + name: Copy of Generating a single cell matrix using Alevin 1.9 shared by user ksuderman + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:transcriptomics + - name:singlecell + - name:training + tools: + - Cut1 + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - join1 + - dropletutils_read_10x + - sceasy_convert + - _dropletBarcodePlot + - dropletutils_empty_drops + update_time: '2023-08-24' + versions: 1 +- create_time: '2023-08-22' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 58a91a914e381dcf + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=58a91a914e381dcf + name: Quality filtering fastq file workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2023-08-22' + versions: 0 +- create_time: '2023-08-18' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: eccaebba0605d876 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=eccaebba0605d876 + name: Workflow constructed from history 'Mouse chromosome 7' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2023-08-18' + versions: 0 +- create_time: '2023-08-16' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: cd3bce36b6ef073d + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=cd3bce36b6ef073d + name: Fastq quality data trimming + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2023-08-16' + versions: 1 +- create_time: '2023-08-09' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Genome visualisation + - Variant calling + - Phylogenetic tree generation + edam_topic: [] + id: 5674956f5c18b85b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5674956f5c18b85b + name: shiv + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - jbrowse + - snippy + update_time: '2023-08-09' + versions: 0 +- create_time: '2023-07-31' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 0555313573cd1ee2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0555313573cd1ee2 + name: QC and filtering + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2023-08-04' + versions: 0 +- create_time: '2023-08-01' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 037c3a9d872be3de + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=037c3a9d872be3de + name: Next Generation Sequencing + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_sort + - trimmomatic + - hisat2 + update_time: '2023-08-01' + versions: 9 +- create_time: '2023-01-19' + creators: + - MTG Lab + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4dbac8374419d29e + latest_version: 12 + license: null + link: https://usegalaxy.org/published/workflow?id=4dbac8374419d29e + name: MOM.v1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - Cut1 + - vcf2tsv + - tp_grep_tool + - tp_sed_tool + - tp_awk_tool + - tp_tail_tool + - tp_easyjoin_tool + - snpEff + - picard_MarkDuplicates + - bcftools_reheader + - freebayes + - bwa_mem + update_time: '2023-07-22' + versions: 12 +- create_time: '2023-07-18' + creators: + - Wendi Bacon + - Julia Jakiela + doi: '' + edam_operation: + - Sequence composition calculation + - RNA-Seq quantification + - Gene expression analysis + edam_topic: [] + id: 1fe6b25825d9b736 + latest_version: 0 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736 + name: Generating a single cell matrix using Alevin 1.9 + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:transcriptomics + - name:singlecell + - name:training + tools: + - Cut1 + - alevin + - _salmon_kallisto_mtx_to_10x + - _ensembl_gtf2gene_list + - join1 + - dropletutils_read_10x + - sceasy_convert + - _dropletBarcodePlot + - dropletutils_empty_drops + update_time: '2023-07-18' + versions: 0 +- create_time: '2023-07-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5efe288b18c7d0ab + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5efe288b18c7d0ab + name: GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: + - sequence-analysis + tools: + - fastqc + - trim_galore + - samtools_stats + - jbrowse + - multiqc + - bowtie2 + update_time: '2023-07-16' + versions: 0 +- create_time: '2023-06-27' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: 63adc811e3ae529d + latest_version: 44 + license: null + link: https://usegalaxy.org/published/workflow?id=63adc811e3ae529d + name: 454_quality_aligned + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cshl_fasta_formatter + - fastq_to_fasta_python + - 'EMBOSS: transeq101' + - fasta_merge_files_and_filter_unique_sequences + - tp_sed_tool + - bioext_bam2msa + - minimap2 + - cshl_fastq_quality_filter + - bioext_bealign + update_time: '2023-07-10' + versions: 44 +- create_time: '2023-07-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ac19037db14fd2de + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=ac19037db14fd2de + name: Build_Exclusion_List_MOM_workflow_v1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - tp_cat + - tp_uniq_tool + - tp_grep_tool + - tp_awk_tool + update_time: '2023-07-06' + versions: 6 +- create_time: '2023-06-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c9a8fd89224e7414 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=c9a8fd89224e7414 + name: sars-cov-2-genome + number_of_steps: null + source: https://usegalaxy.org + tags: + - sequence-analysis + tools: + - fastqc + - jbrowse + - bwa_mem + update_time: '2023-07-01' + versions: 2 +- create_time: '2023-06-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 53d65fd38b9b8c1b + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=53d65fd38b9b8c1b + name: sars-cov-2-genome + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - jbrowse + - bwa_mem + update_time: '2023-06-29' + versions: 3 +- create_time: '2023-06-22' + creators: + - Roberth Anthony Rojas Chavez + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: 4884918895db9af0 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=4884918895db9af0 + name: HIV Codon alignment Bypass + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cshl_fasta_formatter + - filter_by_fasta_ids + - tp_sed_tool + - bioext_bam2msa + - 'EMBOSS: transeq101' + update_time: '2023-06-22' + versions: 2 +- create_time: '2023-06-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0fb89e9c397c8938 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938 + name: Workflow constructed from history 'Copy of 'HPA_lig'' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - get_pdb + - ambertools_acpype + - gmx_sim + - gmx_editconf + - gmx_energy + - gmx_em + - gmx_setup + - tp_grep_tool + - gmx_solvate + - gmx_merge_topology_files + - md_converter + - openbabel_compound_convert + update_time: '2023-06-20' + versions: 1 +- create_time: '2023-06-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c88fe3dc11bc4905 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c88fe3dc11bc4905 + name: Workflow constructed from history 'generate training material' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - addValue + - fasta2tab + - fasta_compute_length + update_time: '2023-06-12' + versions: 0 +- create_time: '2023-06-02' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + edam_topic: [] + id: 544ce8ff6c9f6d4c + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=544ce8ff6c9f6d4c + name: Module 7.2 part 1 (Trimmomatic + HISAT2 + featureCounts) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - featurecounts + - hisat2 + update_time: '2023-06-05' + versions: 6 +- create_time: '2021-10-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9fc9f1db50019929 + latest_version: 2 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9fc9f1db50019929 + name: 'COGCZ:: COVID-19: variation analysis on ARTIC PE data' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + - testingmaximus + - name:v2.1.0+galaxy3 + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2023-05-30' + versions: 2 +- create_time: '2023-05-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 9e74e3455e47c813 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=9e74e3455e47c813 + name: Workflow constructed from history 'Project TEAM3' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fasterq_dump + - cutadapt + - __FLATTEN__ + - multiqc + - bowtie2 + - featurecounts + - deseq2 + update_time: '2023-05-24' + versions: 0 +- create_time: '2023-05-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Cross-assembly + - Mapping assembly + - Genome assembly + - Sequence composition calculation + - De-novo assembly + - Sequencing quality control + edam_topic: [] + id: 5626a440a5798458 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=5626a440a5798458 + name: Workflow constructed from history 'Fungal targeted sequencing analysis Barcode_2' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - porechop + - flye + update_time: '2023-05-22' + versions: 2 +- create_time: '2023-03-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 8e32b0a5a141543e + latest_version: 28 + license: null + link: https://usegalaxy.org/published/workflow?id=8e32b0a5a141543e + name: Basic Chip-Seq Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + - ChIP-Seq + - ChIPSeq + tools: + - fastqc + - trim_galore + - macs2_callpeak + - hisat2 + update_time: '2023-05-21' + versions: 28 +- create_time: '2023-05-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: ac8b74b911778fbc + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ac8b74b911778fbc + name: eab_gse119919 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fasterq_dump + - cutadapt + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-05-17' + versions: 0 +- create_time: '2023-05-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - RNA-Seq analysis + - Sequence trimming + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 734e08331f8f34b7 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=734e08331f8f34b7 + name: Rna-seq pipeline of PML knock-outs against WT + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - join1 + - fasterq_dump + - salmon + - tp_tail_tool + - tp_replace_in_column + - tp_find_and_replace + - fastq_groomer + - limma_voom + - Remove beginning1 + - trim_galore + - melt + - tp_cut_tool + - gprofiler_gost + - Filter1 + - gffread + - Cut1 + - column_order_header_sort + update_time: '2023-05-15' + versions: 2 +- create_time: '2023-05-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0135ec6af1f3be93 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0135ec6af1f3be93 + name: WF SNPs over Exons (cr2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - tp_sort_header_tool + update_time: '2023-05-10' + versions: 1 +- create_time: '2023-05-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: aac2ae0419f7d515 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515 + name: "RNA_SEQ_Germ\xE1n_Vallejo" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - trim_galore + - fasterq_dump + - salmon + - column_order_header_sort + - tp_cut_tool + - limma_voom + update_time: '2023-05-03' + versions: 1 +- create_time: '2023-05-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a89def2c2462674a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a89def2c2462674a + name: RNA_Seq exercice + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - trim_galore + - fasterq_dump + - salmon + - column_order_header_sort + - tp_cut_tool + - limma_voom + update_time: '2023-05-01' + versions: 1 +- create_time: '2023-05-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 93650de42fb8c015 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=93650de42fb8c015 + name: Copy of RNA_Seq exercice + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - trim_galore + - fasterq_dump + - salmon + - column_order_header_sort + - tp_cut_tool + - limma_voom + update_time: '2023-05-01' + versions: 0 +- create_time: '2023-04-25' + creators: [] + doi: '' + edam_operation: + - Mapping + - Peak calling + - Enrichment analysis + - Gene regulatory network analysis + edam_topic: [] + id: 59d34b4f0178120b + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=59d34b4f0178120b + name: ' LFY-tutorial-workflow' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deeptools_plot_heatmap + - deeptools_compute_matrix + - idr + - deeptools_multi_bam_summary + - deeptools_plot_fingerprint + - deeptools_plot_correlation + - macs2_callpeak + - meme_chip + - bedtools_getfastabed + update_time: '2023-04-25' + versions: 4 +- create_time: '2023-04-18' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 58ceaed0a42fe60a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=58ceaed0a42fe60a + name: QC and filtering + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2023-04-18' + versions: 0 +- create_time: '2023-04-05' + creators: [] + doi: '' + edam_operation: + - Validation + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 0930f955bdac93e8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0930f955bdac93e8 + name: mRNA Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - salmon + - volcanoplot + - multiqc + - __MERGE_COLLECTION__ + - deseq2 + - Filter1 + update_time: '2023-04-05' + versions: 0 +- create_time: '2023-03-22' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 79a282b2bf89c6ac + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=79a282b2bf89c6ac + name: Exploring Iris datset with statistics and scatterplots + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2023-03-27' + versions: 2 +- create_time: '2023-03-22' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Read mapping + edam_topic: [] + id: d72e33effe07de02 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=d72e33effe07de02 + name: RNA-seq differential expression analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - bowtie2 + - deseq2 + update_time: '2023-03-27' + versions: 2 +- create_time: '2023-03-22' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 88f8feaad0f615de + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=88f8feaad0f615de + name: exploring iris dataset + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2023-03-24' + versions: 4 +- create_time: '2023-03-24' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 2ceff2cf26eae4cd + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2ceff2cf26eae4cd + name: Alternate pathway + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - snpsift_vartype + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - bowtie2 + - samtool_filter2 + - freebayes + update_time: '2023-03-24' + versions: 1 +- create_time: '2023-03-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 26c4909f2f3df704 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=26c4909f2f3df704 + name: Alignment, variant calling and filtering - AG + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - snpsift_vartype + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-03-24' + versions: 0 +- create_time: '2023-03-22' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: a253589432a44e5a + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=a253589432a44e5a + name: Exploring Iris dataset with statistics and scatterplots + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2023-03-22' + versions: 3 +- create_time: '2023-03-06' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 30a3744026ad86a7 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=30a3744026ad86a7 + name: Find Exons With The Highest Number Of Features + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2023-03-06' + versions: 1 +- create_time: '2021-04-23' + creators: + - Guerler + doi: '' + edam_operation: [] + edam_topic: [] + id: d73c60e406aff265 + latest_version: 11 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d73c60e406aff265 + name: Intra-genome interaction prediction + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - spring_model_all + - collection_element_identifiers + - __FILTER_FAILED_DATASETS__ + - hhsearch + - rbc_splitfasta + - spring_minz + - ffindex_dbkit_create + update_time: '2023-03-06' + versions: 11 +- create_time: '2023-02-27' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: b2f3d7e4cd4d0f11 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=b2f3d7e4cd4d0f11 + name: mothur_thru_Unique.seqs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_unique_seqs + - mothur_align_seqs + update_time: '2023-02-28' + versions: 1 +- create_time: '2022-05-23' + creators: + - Daniel Leon Nahmias + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 18c6e87a884fb5ed + latest_version: 25 + license: null + link: https://usegalaxy.org/published/workflow?id=18c6e87a884fb5ed + name: exom_trio_best_workflow_ever + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - varscan_mpileup + - trim_galore + - snpEff + - snpSift_annotate + - samtools_mpileup + - bwa_mem + update_time: '2023-02-27' + versions: 25 +- create_time: '2023-02-25' + creators: + - null + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Statistical calculation + - Taxonomic classification + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: badd4b56dbdeaba7 + latest_version: 12 + license: null + link: https://usegalaxy.org/published/workflow?id=badd4b56dbdeaba7 + name: Nanopore MinION - 16s Data Analysis Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: + - MinION + - Nanopore + tools: + - fastqc + - fastp + - collection_column_join + - kraken2 + - porechop + - multiqc + update_time: '2023-02-25' + versions: 12 +- create_time: '2023-02-23' + creators: [] + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 93810012f2610de4 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=93810012f2610de4 + name: SRA list from "NCBI run selector" to a single FASTA file + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasterq_dump + - fasta_merge_files_and_filter_unique_sequences + - fastq_to_fasta_python + update_time: '2023-02-23' + versions: 0 +- create_time: '2023-02-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 43cea919ebf9d978 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=43cea919ebf9d978 + name: Hi-C_fastqToPairs_hic (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - hicup2juicer + - compose_text_param + - hicup_hicup + - Filter1 + update_time: '2023-02-23' + versions: 1 +- create_time: '2023-02-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: f21d576695f9fe77 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f21d576695f9fe77 + name: Hi-C_juicermediumtabixToCool_c (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_balance + - cooler_makebins + - cooler_cload_tabix + update_time: '2023-02-23' + versions: 1 +- create_time: '2023-02-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 06eaa5b141fe7a08 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=06eaa5b141fe7a08 + name: cHi-C_fastqToCool_hicup_c (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + - compose_text_param + - Filter1 + update_time: '2023-02-23' + versions: 1 +- create_time: '2023-02-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Visualisation + edam_topic: [] + id: 1dc312e3fba9f810 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1dc312e3fba9f810 + name: Hi-C_fastqToCool_hicup_c (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - Hi-C + tools: + - cooler_csort_tabix + - pygenomeTracks + update_time: '2023-02-23' + versions: 1 +- create_time: '2023-02-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 842c09b49c456429 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=842c09b49c456429 + name: CUTandRUN (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-02-23' + versions: 1 +- create_time: '2023-02-19' + creators: + - Bill Gao + doi: '' + edam_operation: + - Formatting + - Sequence alignment + edam_topic: [] + id: 52e20808e37c8afd + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=52e20808e37c8afd + name: SNP bam from human DE FASTQ + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_view + - picard_MarkDuplicates + - picard_AddOrReplaceReadGroups + - hisat2 + update_time: '2023-02-19' + versions: 2 +- create_time: '2023-02-19' + creators: + - Bill Gao + doi: '' + edam_operation: + - Formatting + - Sequence alignment + edam_topic: [] + id: 5c4ce4a781317ebb + latest_version: 18 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=5c4ce4a781317ebb + name: SNP bam from human SE FASTQ + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_view + - picard_MarkDuplicates + - picard_AddOrReplaceReadGroups + - hisat2 + update_time: '2023-02-19' + versions: 18 +- create_time: '2023-01-27' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence trimming + - Read summarisation + - RNA-Seq quantification + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 8ebcae16a7822d93 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=8ebcae16a7822d93 + name: Copy and aNNOTATED wORKFLOW rnaSEQ + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - cutadapt + - rna_star + - multiqc + - featurecounts + update_time: '2023-02-04' + versions: 2 +- create_time: '2023-01-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6dada297572d77bd + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=6dada297572d77bd + name: Workflow 123 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sailfish + - trim_galore + - multiqc + - deseq2 + update_time: '2023-01-31' + versions: 0 +- create_time: '2023-01-30' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 271b97e5c00c4da4 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=271b97e5c00c4da4 + name: RNA-seq for bacteria + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - __FLATTEN__ + - multiqc + - featurecounts + - hisat2 + update_time: '2023-01-30' + versions: 1 +- create_time: '2023-01-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 53834a5fb46ca0f6 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=53834a5fb46ca0f6 + name: How to workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sailfish + - trim_galore + - multiqc + - deseq2 + update_time: '2023-01-25' + versions: 3 +- create_time: '2023-01-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4054ceeba1a2fa69 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4054ceeba1a2fa69 + name: Bioinformatics Assignment + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-24' + versions: 0 +- create_time: '2023-01-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6a08af55c086ec62 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=6a08af55c086ec62 + name: Bioinformatics Data Handling Assignment 2022 corrected + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - picard_MarkDuplicatesWithMateCigar + - bam_to_sam + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - vcffilter2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-24' + versions: 0 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 778a8867b0a6ea4f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=778a8867b0a6ea4f + name: RNAseq_PE (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 1f28e673ea725541 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=1f28e673ea725541 + name: RNAseq_PE (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 63f61ad7cae40646 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=63f61ad7cae40646 + name: ChIPseq_SR (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c74e3a24751d9924 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c74e3a24751d9924 + name: RNAseq_SR (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e42a07b777c9f9dc + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e42a07b777c9f9dc + name: ATACseq (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7cee34a6c06c21e4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7cee34a6c06c21e4 + name: ChIPseq_PE (release v0.3) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: d4029ce1344e874a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d4029ce1344e874a + name: ATACseq (release v0.4) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-12' + creators: + - '' + - Lutimba Stuart + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Mapping + - Read mapping + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Variant calling + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: eb4b32fcf4a9f64a + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a + name: 'RNAseq-Analysis WorkFlow ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - deg_annotate + - trimmomatic + - rseqc_tin + - cshl_fastq_quality_boxplot + - gatk4_mutect2 + - bowtie2 + - featurecounts + - bedtools_bamtobed + - samtools_sort + - trim_galore + - vcfgeno2haplo + - multiqc + - deseq2 + - vcfcheck + - bcftools_cnv + - samtools_markdup + - fastq_info + - samtools_flagstat + - freebayes + - fastq_stats + - rseqc_read_distribution + - samtools_view + update_time: '2023-01-12' + versions: 7 +- create_time: '2022-07-05' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 8ed3444a692f8e61 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8ed3444a692f8e61 + name: Copy of amp-seq_treatment shared by user kyakuno + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_join + update_time: '2023-01-12' + versions: 0 +- create_time: '2022-11-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e6f57346a02be07f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e6f57346a02be07f + name: dvkworkflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-10' + versions: 0 +- create_time: '2023-01-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: d761637d43ee0324 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=d761637d43ee0324 + name: workflow test + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - stringtie + - edger + - samtools_view + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-01-10' + versions: 1 +- create_time: '2023-01-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6d8f0be547b12528 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=6d8f0be547b12528 + name: ' ''BIOINFORMATICS: NGS PIPELINE_New History_workflow''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff_download + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - bcftools_plugin_counts + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-09' + versions: 0 +- create_time: '2023-01-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 78979ec454b98338 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=78979ec454b98338 + name: ' BIOINFORMATICS: NGS PIPELINE_workflow' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - bcftools_plugin_counts + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-09' + versions: 0 +- create_time: '2023-01-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - 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Summary_Statistics1 + - vcffilter2 + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - snpEff_databases + - snpEff_download + - snpEff + - samtools_flagstat + - snpsift_vartype + - samtool_filter2 + - bwa_mem + - freebayes + - Filter1 + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2023-01-06' + versions: 12 +- create_time: '2023-01-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 692a2b0bb818336d + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=692a2b0bb818336d + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL - using + wANNOVAR' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - 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Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-05' + versions: 0 +- create_time: '2023-01-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f63f7a0a33a83841 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f63f7a0a33a83841 + name: Workflow constructed from history 'K22063917 Assignment -wANNOVAR and SnpEffeff + & SnpSift in one history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - snpSift_filter + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-05' + versions: 0 +- create_time: '2023-01-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 21a047a4e068860f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=21a047a4e068860f + name: Workflow constructed from history 'K22063917 Assignment using a different + aligner Bowtie2' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - vcfvcfintersect + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - picard_MarkDuplicates + - bedtools_coveragebed + - samtools_flagstat + - Summary_Statistics1 + - Filter1 + - bowtie2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-04' + versions: 0 +- create_time: '2023-01-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d314df52f2f51502 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d314df52f2f51502 + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL - using + wANNOVAR' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-04' + versions: 0 +- create_time: '2023-01-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 8c1516493c55bf7d + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8c1516493c55bf7d + name: Workflow constructed from history 'K22063917 Assignment -wANNOVAR and SnpEffeff + & SnpSift in one history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - snpSift_filter + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-04' + versions: 0 +- create_time: '2022-12-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Gene prediction + - Genome annotation + - Coding region prediction + - Genome assembly + - Sequence composition calculation + - Aggregation + - Sequencing quality control + edam_topic: [] + id: b43b72dcf5f7694d + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=b43b72dcf5f7694d + name: 'H. Somni Workflow ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - unicycler + - prokka + - export_remote + update_time: '2023-01-03' + versions: 9 +- create_time: '2023-01-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 28abac549697f65a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=28abac549697f65a + name: Workflow constructed from history 'K22063917 Assignment -wANNOVAR and SnpEffeff + & SnpSift in one history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - snpSift_filter + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-03' + versions: 0 +- create_time: '2023-01-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f0feca8af9aeddba + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f0feca8af9aeddba + name: Workflow constructed from history ''K22063917 Assignment FINAL - SnpEffeff + to anotate & SnpSift to filter' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - snpSift_filter + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-03' + versions: 0 +- create_time: '2023-01-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 89660361d4121fa8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=89660361d4121fa8 + name: Workflow constructed from history 'K22063917 Assignment FINAL - SnpEffeff' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-02' + versions: 0 +- create_time: '2023-01-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 8b133c1d302c8681 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8b133c1d302c8681 + name: Workflow constructed from history 'k22063917 NGS0001 Assignment FINAL' - up + to variant calling & filtering' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-02' + versions: 0 +- create_time: '2023-01-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d196c3bde666eccb + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d196c3bde666eccb + name: Workflow constructed from history 'K22063917 Assignment using a different + aligner Bowtie2' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - vcfvcfintersect + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - picard_MarkDuplicates + - bedtools_coveragebed + - samtools_flagstat + - Summary_Statistics1 + - Filter1 + - bowtie2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-02' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4d0607d3589e0775 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4d0607d3589e0775 + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL -wANNOVAR + and SnpEffeff in one history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 02c96a9c6bb708ac + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=02c96a9c6bb708ac + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL - using + wANNOVAR' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2e65bc5f9d9f2a75 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=2e65bc5f9d9f2a75 + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL -wANNOVAR + and SnpEffeff in one history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f302d673420a9bdd + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f302d673420a9bdd + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL -wANNOVAR + and SnpEffeff in one history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 86b802ea75d18160 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=86b802ea75d18160 + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL - using + wANNOVAR' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - bcftools_stats + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ced446bf2428497b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ced446bf2428497b + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL -wANNOVAR + and SnpEffeff in one history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 39e79458c9ba581c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=39e79458c9ba581c + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL - using + wANNOVAR' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d2edc47cc7963885 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d2edc47cc7963885 + name: Workflow constructed from history 'K22063917 Assignment attempt FINAL - using + wANNOVAR' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a98a3ac1a41752bc + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a98a3ac1a41752bc + name: Workflow constructed from history 'K22063917 Assignment using Bowtie2 up to + VCF VCF intersect - final' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - vcfvcfintersect + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f9d546aae406cf15 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f9d546aae406cf15 + name: Workflow constructed from history 'K22063917 Assignment using a different + aligner Bowtie2' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - vcfvcfintersect + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - picard_MarkDuplicates + - bedtools_coveragebed + - samtools_flagstat + - Summary_Statistics1 + - Filter1 + - bowtie2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 262ab42118016c41 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=262ab42118016c41 + name: Workflow K22063917 Assignment using Bowtie2 up to VCF VCF intersect - final + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - vcfvcfintersect + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b461ac6f18e0c9cf + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b461ac6f18e0c9cf + name: Workflow K22063917 Assignment using a different aligner Bowtie2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - vcfvcfintersect + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - picard_MarkDuplicates + - bedtools_coveragebed + - samtools_flagstat + - Summary_Statistics1 + - Filter1 + - bowtie2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ba405b449e27ba37 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ba405b449e27ba37 + name: Workflow 'K22063917 Assignment attempt FINAL -wANNOVAR and SnpEffeff in one + workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b8804291f2754fc8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b8804291f2754fc8 + name: Workflow 'K22063917 Assignment FINAL - SnpEffeff' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2023-01-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3dc57709c4387ba7 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=3dc57709c4387ba7 + name: Workflow 'k22063917 NGS0001 Assignment FINAL' - up to variant calling & filtering' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2023-01-01' + versions: 0 +- create_time: '2022-12-26' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Data handling + - Sequencing quality control + edam_topic: [] + id: 0a3513961f0cf9dd + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0a3513961f0cf9dd + name: WorkFlowDaniAnchuela + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fasterq_dump + - trimmer + update_time: '2022-12-28' + versions: 1 +- create_time: '2022-12-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 427fce51fd9508eb + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=427fce51fd9508eb + name: myfirstWFDANIANCHUELA + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - Show tail1 + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - salmon + - __RELABEL_FROM_FILE__ + - Grep1 + - limma_voom + update_time: '2022-12-28' + versions: 7 +- create_time: '2022-12-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 228ae7f537a60226 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=228ae7f537a60226 + name: DaniAnchuelaWF + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - salmon + - __RELABEL_FROM_FILE__ + - tp_tail_tool + - limma_voom + update_time: '2022-12-28' + versions: 4 +- create_time: '2022-12-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 46e4acdc08eb3ea5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=46e4acdc08eb3ea5 + name: Copy of 'Bioinformatics assessment' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - snpSift_filter + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - snpSift_annotate + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-12-27' + versions: 0 +- create_time: '2022-12-22' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Read pre-processing + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Primer removal + edam_topic: [] + id: 7b9f36ae2174164a + latest_version: 12 + license: null + link: https://usegalaxy.org/published/workflow?id=7b9f36ae2174164a + name: Varyant Cagirma 2022 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bwa + - cutadapt + - samtools_view + - bcftools_call + - bcftools_mpileup + update_time: '2022-12-22' + versions: 12 +- create_time: '2022-12-12' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 0d6a4dfbccafd2a2 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0d6a4dfbccafd2a2 + name: Workflow introduction to Galaxy, Klaudia, 12-12-2022 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2022-12-12' + versions: 1 +- create_time: '2022-12-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Annotation + - Sequencing quality control + edam_topic: [] + id: 5944c5effd56b0d6 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6 + name: Workflow constructed from history 'RNA Seq week 3' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - annotatemyids + - Cut1 + - fasterq_dump + - rseqc_geneBody_coverage + - volcanoplot + - cutadapt + - limma_voom + - multiqc + - featurecounts + - hisat2 + update_time: '2022-12-08' + versions: 0 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 93e69c7e7a857ca3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=93e69c7e7a857ca3 + name: RNAseq_PE (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 676b88d0aac13fa5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=676b88d0aac13fa5 + name: RNAseq_SR (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3fc5bdbd6355477c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3fc5bdbd6355477c + name: ChIPseq_SR (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 907aaf55487ddf43 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=907aaf55487ddf43 + name: ATACseq (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e12296df7cf33c69 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e12296df7cf33c69 + name: ChIPseq_PE (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c156e67ad1ae4a97 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c156e67ad1ae4a97 + name: CUTandRUN (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-11-30' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: cf9069dd5d24d58f + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=cf9069dd5d24d58f + name: Find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2022-11-30' + versions: 1 +- create_time: '2022-11-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 7a203cf1678df56d + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=7a203cf1678df56d + name: ' RNAseq Analysis for Project 3' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-11-30' + versions: 3 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2e92cca68b7979f6 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=2e92cca68b7979f6 + name: 'NrD Workflow: 12 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2022-11-30' + versions: 5 +- create_time: '2022-11-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 30883502ec515fe2 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=30883502ec515fe2 + name: RNAseq Analysis for SRR2221833 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-11-30' + versions: 4 +- create_time: '2022-11-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 63d590e8567f7157 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=63d590e8567f7157 + name: RNAseq Analysis for SRR2221837 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-11-30' + versions: 2 +- create_time: '2022-11-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: e5a01f746bc9e9b5 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e5a01f746bc9e9b5 + name: RNAseq Analysis for SRR2221841 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-11-30' + versions: 1 +- create_time: '2022-11-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 75f14618020c922a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=75f14618020c922a + name: RNAseq Analysis for SRR2221845 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-11-30' + versions: 1 +- create_time: '2022-11-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 13460c791ca97689 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=13460c791ca97689 + name: RNAseq Analysis for SRR2221849 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-11-30' + versions: 1 +- create_time: '2022-11-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: f961fc46d4fddecc + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=f961fc46d4fddecc + name: RNAseq Analysis for SRR2221853 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-11-30' + versions: 1 +- create_time: '2021-07-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4a3057fdc10d843c + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=4a3057fdc10d843c + name: PNGS Convertion + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sed_tool + update_time: '2022-11-28' + versions: 8 +- create_time: '2022-11-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5ffeb9904cf5f0bf + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5ffeb9904cf5f0bf + name: Alignment_Varint_Calling_and_Filtering-v0.1 EJK + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-11-25' + versions: 0 +- create_time: '2022-10-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 2375a915a5b33b39 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2375a915a5b33b39 + name: RNAseq Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-11-23' + versions: 1 +- create_time: '2022-11-21' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 3e2bbafb8c6580af + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=3e2bbafb8c6580af + name: Project Step 6 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - vcfannotate + - vcffilter2 + - fastq_groomer + - bowtie2 + - freebayes + update_time: '2022-11-21' + versions: 0 +- create_time: '2022-11-10' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 195a608c481040de + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=195a608c481040de + name: dcTMD calculations with GROMACS (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_text_file_with_recurring_lines + - split_file_to_collection + - add_line_to_file + - tp_cat + - gmx_sim + - biomd_neqgamma + - gmx_solvate + - tp_sed_tool + - gmx_makendx + - compose_text_param + - ctb_online_data_fetch + - param_value_from_file + - gmx_em + update_time: '2022-11-10' + versions: 1 +- create_time: '2022-11-05' + creators: [] + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Visualisation + - Genome assembly + - De-novo assembly + - Sequence assembly validation + - Scaffolding + edam_topic: [] + id: 4029a0c8fa23d375 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=4029a0c8fa23d375 + name: Workflow constructed from history 'genome assemblyQC' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - merqury + - meryl + - quast + update_time: '2022-11-05' + versions: 1 +- create_time: '2022-11-03' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Genome indexing + - Read mapping + - Analysis + - Generation + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Read alignment + - Sequence assembly + - Sequence assembly visualisation + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: bff206b4625375bc + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=bff206b4625375bc + name: sweet potato + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - nanoplot + - pilon + - bandage_info + - flye + - fasta-stats + - bandage_image + - bwa_mem + update_time: '2022-11-03' + versions: 1 +- create_time: '2022-11-03' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f3c8093c5b8a7233 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=f3c8093c5b8a7233 + name: RNAseq_PE (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2022-11-03' + versions: 1 +- create_time: '2019-06-27' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Read pre-processing + - Read mapping + - Primer removal + edam_topic: [] + id: a57a4249a8a21a6d + latest_version: 12 + license: null + link: https://usegalaxy.org/published/workflow?id=a57a4249a8a21a6d + name: TnSeq Processing + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cutadapt + - bowtie2 + update_time: '2022-10-31' + versions: 12 +- create_time: '2022-10-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 451b529be8ab5865 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=451b529be8ab5865 + name: 'proteinas ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2022-10-28' + versions: 0 +- create_time: '2022-10-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: fe262214fba1cb8e + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=fe262214fba1cb8e + name: Plantitas Team Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastqe + - cutadapt + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7832cfdeabe47696 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7832cfdeabe47696 + name: ChIPseq_SR (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: afd7633a34d68704 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=afd7633a34d68704 + name: ATACseq (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-27' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 31cc891be77cbc6f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f + name: 'COVID-19: consensus construction (release v0.4)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-23' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: f14121a9358dffdb + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f14121a9358dffdb + name: Question1Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bedtools_intersectbed + update_time: '2022-10-23' + versions: 0 +- create_time: '2022-10-20' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 07e761b2501971c6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=07e761b2501971c6 + name: 'COVID-19: variation analysis reporting (release v0.3)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-10-20' + versions: 1 +- create_time: '2022-10-18' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Pairwise sequence alignment + - Phylogenetic tree analysis + - Phylogenetic tree reconstruction + - Phylogenetic tree generation + edam_topic: [] + id: 0596162a499b4074 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0596162a499b4074 + name: Q1 phylogenetic context analysis + number_of_steps: null + source: https://usegalaxy.org + tags: + - viral + - bacterial + - quickies + - variation + - phylogeny + tools: + - newick_display + - snpSift_extractFields + - Remove beginning1 + - collapse_dataset + - ncbi_acc_download + - rapidnj + - datamash_ops + - lofreq_call + - snpEff_build_gb + - snpEff + - minimap2 + - __MERGE_COLLECTION__ + - bcftools_consensus + update_time: '2022-10-18' + versions: 1 +- create_time: '2022-10-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7c5e8394ce29288d + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=7c5e8394ce29288d + name: Somatics Variant Calling - HDS (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + - varscan_somatic + update_time: '2022-10-07' + versions: 0 +- create_time: '2022-10-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5af0411f48f93628 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=5af0411f48f93628 + name: ' Generation of input-normalized coverage files and their visualization (CHIP)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deeptools_compute_matrix + - deeptools_plot_heatmap + update_time: '2022-10-06' + versions: 4 +- create_time: '2022-09-21' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: e4d260d46b516b4f + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=e4d260d46b516b4f + name: Benchmarking DNA Mappers - PE CHM13 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - minimap2 + - bowtie2 + - bwa_mem + update_time: '2022-09-30' + versions: 6 +- create_time: '2021-12-09' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 8ec186ed3f0470e2 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=8ec186ed3f0470e2 + name: Benchmarking DNA Mappers - PE hg38 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - minimap2 + - hisat2 + - bowtie2 + - bwa_mem + update_time: '2022-09-30' + versions: 7 +- create_time: '2020-02-11' + creators: + - Charles Hadley King + doi: '' + edam_operation: + - Statistical calculation + - Generation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2cbcfeb772f348c9 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=2cbcfeb772f348c9 + name: Galaxy BioCompute Object Development Test + number_of_steps: null + source: https://usegalaxy.org + tags: + - BCO + - HTS + - Testing + - New + - stuff + tools: + - fastqc + - fastq_groomer + - ncbi_acc_download + - bwa_mem + update_time: '2022-09-30' + versions: 3 +- create_time: '2022-09-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cb7c638fed3ed697 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=cb7c638fed3ed697 + name: 'Week 5 Assignment ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - tp_head_tool + - tp_cut_tool + - sort1 + update_time: '2022-09-29' + versions: 5 +- create_time: '2021-04-23' + creators: + - Guerler + doi: '' + edam_operation: [] + edam_topic: [] + id: 929b7a83015fdcda + latest_version: 2 + license: MIT + link: https://usegalaxy.org/published/workflow?id=929b7a83015fdcda + name: Inter-genome interaction prediction + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - spring_model_all + - collection_element_identifiers + - ffindex_dbkit_merge + - __FILTER_FAILED_DATASETS__ + - hhsearch + - rbc_splitfasta + - spring_minz + - ffindex_dbkit_create + update_time: '2022-09-25' + versions: 2 +- create_time: '2022-09-22' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 8e9a94fe8e3fef9d + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=8e9a94fe8e3fef9d + name: Benchmarking DNA Mappers - locust + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - minimap2 + - hisat2 + - bowtie2 + - bwa_mem + update_time: '2022-09-23' + versions: 2 +- create_time: '2022-09-21' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 6d925811544f594b + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=6d925811544f594b + name: Benchmarking DNA Mappers - chicken + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - minimap2 + - hisat2 + - bowtie2 + - bwa_mem + update_time: '2022-09-22' + versions: 2 +- create_time: '2022-09-21' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 2135b0255284752c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=2135b0255284752c + name: Benchmarking DNA Mappers - Elephant + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - minimap2 + - hisat2 + - bowtie2 + - bwa_mem + update_time: '2022-09-22' + versions: 2 +- create_time: '2022-05-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Validation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a37961bf3d435918 + latest_version: 14 + license: null + link: https://usegalaxy.org/published/workflow?id=a37961bf3d435918 + name: NGS Pipeline for Paired End Reads (R1 and R2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - varscan + - naive_variant_caller + - bamleftalign + - multiqc + - picard_MarkDuplicates + - samtools_mpileup + - bwa_mem + update_time: '2022-09-15' + versions: 14 +- create_time: '2022-06-16' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Read pre-processing + - Primer removal + edam_topic: [] + id: 08edef22fa132799 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=08edef22fa132799 + name: TnSeq Data Workflow -SKC + number_of_steps: null + source: https://usegalaxy.org + tags: + - TnSeq + - WilsonLab + tools: + - cshl_fastq_quality_filter + - cutadapt + - trimmer + update_time: '2022-09-12' + versions: 3 +- create_time: '2021-12-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 24ada8b98b04fedc + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc + name: potato ex2 (all) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - cshl_fastx_reverse_complement + - cat1 + - Grep1 + - fastq_to_tabular + - tab2fasta + - cshl_fastq_quality_filter + - fastq_join + - cshl_fastx_renamer + update_time: '2022-09-09' + versions: 5 +- create_time: '2022-08-21' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: ffd718437128bce2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ffd718437128bce2 + name: Workflow constructed from history 'BBL735_IV_Lab1' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2022-08-21' + versions: 0 +- create_time: '2022-08-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fbf75fbb72b488bd + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=fbf75fbb72b488bd + name: '''BBL735_Lab2(Olympic)_AT''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Count1 + - tp_split_on_column + - Cut1 + - tp_sort_header_tool + - Add_a_column1 + - Remove beginning1 + - datamash_ops + - tabular_to_csv + - regexColumn1 + - join1 + - cat1 + - tp_sorted_uniq + - Show beginning1 + - Filter1 + update_time: '2022-08-21' + versions: 2 +- create_time: '2022-04-10' + creators: [] + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: e067c4e66f0af362 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=e067c4e66f0af362 + name: Sample Workflow for 16s Bacterial Sequencing + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - dada2_makeSequenceTable + - table_compute + - __UNZIP_COLLECTION__ + - __FILTER_FAILED_DATASETS__ + - dada2_assignTaxonomyAddspecies + - __SORTLIST__ + - dada2_filterAndTrim + - dada2_mergePairs + - dada2_learnErrors + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2022-08-02' + versions: 3 +- create_time: '2022-07-24' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 2b0d73370a1577b4 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2b0d73370a1577b4 + name: Workflow history 'Mapping Class 3' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bowtie2 + update_time: '2022-07-24' + versions: 1 +- create_time: '2022-07-13' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - RNA-Seq analysis + - Transcriptome assembly + - Generation + - Sequence alignment + edam_topic: [] + id: ef2c1fb7d6a51b3a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ef2c1fb7d6a51b3a + name: Benchmarking DNA Cloud Costs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - stringtie + - bwa_mem + - bwa + - bowtie2 + - hisat2 + update_time: '2022-07-13' + versions: 0 +- create_time: '2022-07-05' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: d7a11a4dfda3dab4 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=d7a11a4dfda3dab4 + name: 'Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With + Mothur] (imported from uploaded file)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - metagenomics + tools: + - mothur_screen_seqs + - mothur_unique_seqs + - mothur_summary_seqs + - mothur_count_seqs + update_time: '2022-07-09' + versions: 3 +- create_time: '2022-07-03' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: d653eaefcf6b4697 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697 + name: Workflow constructed from history 'MICROBIAL ANALYSIS (16s)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - mothur_heatmap_sim + - mothur_make_biom + - mothur_cluster + - mothur_rarefaction_single + - mothur_align_seqs + - mothur_classify_seqs + - mothur_venn + - taxonomy_krona_chart + - mothur_get_groups + - mothur_seq_error + - mothur_make_shared + - newick_display + - mothur_remove_groups + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_dist_shared + - mothur_dist_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_tree_shared + - mothur_unique_seqs + - mothur_classify_otu + - mothur_taxonomy_to_krona + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - XY_Plot_1 + - mothur_count_groups + - mothur_cluster_split + - mothur_sub_sample + - mothur_pre_cluster + update_time: '2022-07-03' + versions: 0 +- create_time: '2022-07-03' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: 775335812a6b7a61 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=775335812a6b7a61 + name: Workflow constructed from history '16S Microbial Analysis' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - mothur_heatmap_sim + - mothur_make_biom + - mothur_cluster + - mothur_rarefaction_single + - mothur_align_seqs + - mothur_classify_seqs + - mothur_venn + - taxonomy_krona_chart + - mothur_get_groups + - mothur_seq_error + - mothur_make_shared + - newick_display + - mothur_remove_groups + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_dist_shared + - mothur_dist_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_tree_shared + - mothur_unique_seqs + - mothur_classify_otu + - mothur_taxonomy_to_krona + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - XY_Plot_1 + - mothur_count_groups + - mothur_cluster_split + - mothur_sub_sample + - mothur_pre_cluster + update_time: '2022-07-03' + versions: 0 +- create_time: '2022-06-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: aaec757e04605d3a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=aaec757e04605d3a + name: Create GRO and TOP complex files (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - ambertools_acpype + - Cut1 + - ctb_rdkit_descriptors + - gmx_setup + - tp_grep_tool + - gmx_merge_topology_files + - param_value_from_file + - ambertools_antechamber + - openbabel_compound_convert + update_time: '2022-06-30' + versions: 1 +- create_time: '2022-06-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 00a4dbc9329c638b + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=00a4dbc9329c638b + name: Create GRO and TOP complex files (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - ambertools_acpype + - Cut1 + - ctb_rdkit_descriptors + - gmx_setup + - tp_grep_tool + - gmx_merge_topology_files + - param_value_from_file + - ambertools_antechamber + - openbabel_compound_convert + update_time: '2022-06-30' + versions: 1 +- create_time: '2022-06-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 183254b3565bcb04 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=183254b3565bcb04 + name: MMGBSA calculations with GROMACS (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2022-06-30' + versions: 1 +- create_time: '2022-06-30' + creators: + - Simon Bray + doi: '' + edam_operation: [] + edam_topic: [] + id: 3c1e2bbb1a77cc30 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30 + name: MMGBSA calculations with GROMACS (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_text_file_with_recurring_lines + - mmpbsa_mmgbsa + - split_file_to_collection + - collapse_dataset + - Cut1 + - gmx_sim + - gmx_em + - parmconv + - gmx_solvate + - tp_grep_tool + - compose_text_param + - Summary_Statistics1 + - md_converter + - param_value_from_file + - gmx_editconf + update_time: '2022-06-30' + versions: 1 +- create_time: '2022-03-09' + creators: [] + doi: '' + edam_operation: + - Validation + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 0ee0493f3168cbb3 + latest_version: 16 + license: null + link: https://usegalaxy.org/published/workflow?id=0ee0493f3168cbb3 + name: NGS_Workflow_CPBroutineNEW + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - varscan_mpileup + - ivar_variants + - naive_variant_caller + - multiqc + - samtools_mpileup + - bowtie2 + - freebayes + update_time: '2022-06-21' + versions: 16 +- create_time: '2020-12-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 73d98e5f821a78b3 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=73d98e5f821a78b3 + name: Kaspar RNA-Seq Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - tp_cat + - fastq_quality_trimmer + - fastq_groomer + - bowtie2 + - featurecounts + update_time: '2022-06-21' + versions: 8 +- create_time: '2019-03-29' + creators: [] + doi: '' + edam_operation: + - Peak calling + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + edam_topic: [] + id: fe2d15d352a9919f + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=fe2d15d352a9919f + name: Mahesh Hegde Chip Seq Default + number_of_steps: null + source: https://usegalaxy.org + tags: + - Chipseq + tools: + - wig_to_bigWig + - fastq_groomer + - bowtie2 + - macs2_callpeak + update_time: '2022-06-16' + versions: 4 +- create_time: '2022-06-16' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 14dc039ee7138b8b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org/published/workflow?id=14dc039ee7138b8b + name: Quality Evaluation (release v0.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - meryl + - genomescope + update_time: '2022-06-16' + versions: 1 +- create_time: '2022-06-08' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Pairwise sequence alignment + - Phylogenetic tree analysis + - Phylogenetic tree reconstruction + - Phylogenetic tree generation + edam_topic: [] + id: 005924662f68a480 + latest_version: 14 + license: null + link: https://usegalaxy.org/published/workflow?id=005924662f68a480 + name: Q1 phylogenetic context analysis + number_of_steps: null + source: https://usegalaxy.org + tags: + - viral + - bacterial + - quickies + - variation + - phylogeny + tools: + - newick_display + - snpSift_extractFields + - Remove beginning1 + - collapse_dataset + - ncbi_acc_download + - rapidnj + - datamash_ops + - lofreq_call + - snpEff_build_gb + - snpEff + - minimap2 + - __MERGE_COLLECTION__ + - bcftools_consensus + update_time: '2022-06-14' + versions: 14 +- create_time: '2022-06-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Generation + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 8c4fcd4bd9d5a72d + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=8c4fcd4bd9d5a72d + name: Clinical Genetics Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gtftobed12 + - bcftools_plugin_counts + - bwa + - bedtools_intersectbed + - Grep1 + - vcffilter2 + - bcftools_call + - bcftools_mpileup + update_time: '2022-06-09' + versions: 13 +- create_time: '2022-03-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq analysis + - Transcriptome assembly + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b1b75a9323d25085 + latest_version: 25 + license: null + link: https://usegalaxy.org/published/workflow?id=b1b75a9323d25085 + name: Benchmarking RNA-seq Cloud Costs-Paired + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_sort + - stringtie + - qualimap_rnaseq + - umi_tools_count + - salmon + - fastq_paired_end_deinterlacer + - rna_star + - deeptools_bam_coverage + update_time: '2022-06-07' + versions: 25 +- create_time: '2022-05-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: d136d24e4c96962a + latest_version: 3 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d136d24e4c96962a + name: Generic consensus construction from VCF calls + number_of_steps: null + source: https://usegalaxy.org + tags: + - mlxv + - generic + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-06-03' + versions: 3 +- create_time: '2022-05-03' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 4b7e73bb7ac93c95 + latest_version: 14 + license: null + link: https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95 + name: 'NGS analyses: biocontainment 230-320bp' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cshl_fastx_reverse_complement + - mothur_fastq_info + - filter_by_fasta_ids + - fastq_to_fasta_python + - cat_multiple + - fasta_merge_files_and_filter_unique_sequences + - fastq_quality_trimmer + - mothur_unique_seqs + - fastq_join + update_time: '2022-06-02' + versions: 14 +- create_time: '2022-06-02' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0fa2ce12c2874b1d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2022-06-02' + versions: 1 +- create_time: '2022-06-02' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d96bd5c9fb553f2c + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2022-06-02' + versions: 1 +- create_time: '2022-06-02' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4b41a8247f52c463 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4b41a8247f52c463 + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2.2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2022-06-02' + versions: 1 +- create_time: '2022-05-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 9e1762e46ddf9a85 + latest_version: 3 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9e1762e46ddf9a85 + name: Genetic variation analysis reporting + number_of_steps: null + source: https://usegalaxy.org + tags: + - mpvx + - generic + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - compose_text_param + - tp_find_and_replace + - Filter1 + update_time: '2022-06-01' + versions: 3 +- create_time: '2022-05-24' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Formatting + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 33ae58f05e5e1d60 + latest_version: 6 + license: MIT + link: https://usegalaxy.org/published/workflow?id=33ae58f05e5e1d60 + name: Generic variation analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.org + tags: + - mpxv + - generic + tools: + - fastp + - lofreq_call + - lofreq_viterbi + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - multiqc + - bwa_mem + update_time: '2022-05-31' + versions: 6 +- create_time: '2022-01-05' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Data handling + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + edam_topic: [] + id: 73ef57dfa532af3d + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=73ef57dfa532af3d + name: NCBI SRA to FPKM + number_of_steps: null + source: https://usegalaxy.org + tags: + - NCBI + - SRA + - FPKM + tools: + - fastq_dump + - stringtie + - trim_galore + - hisat2 + update_time: '2022-05-30' + versions: 1 +- create_time: '2022-05-27' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Coding region prediction + - Genome annotation + - Cross-assembly + - Mapping assembly + - Gene prediction + - Filtering + - Sequencing quality control + edam_topic: [] + id: 7fc8b2398b6f093f + latest_version: 12 + license: null + link: https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f + name: BIOL106_Sp22_Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - jcvi_gff_stats + - flye + - filtlong + - prokka + - ncbi_blastn_wrapper + update_time: '2022-05-28' + versions: 12 +- create_time: '2022-05-16' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + - Nucleic acid sequence analysis + edam_topic: [] + id: 8fb8c80c93ad694e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8fb8c80c93ad694e + name: Copy of RNA seq workflow_JSJ shared by user jogis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - 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COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2022-03-31' + versions: 1 +- create_time: '2021-12-08' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 303af6cec326947c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=303af6cec326947c + name: Benchmarking DNA Cloud Costs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bwa + - hisat2 + - bowtie2 + - bwa_mem + update_time: '2022-03-22' + versions: 2 +- create_time: '2022-03-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c03c18813a3380b3 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c03c18813a3380b3 + name: 'Workflow constructed from history ''RUN FROM START: 3C NUC COMPRESSED''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - 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Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 092be3cf6e40282c + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=092be3cf6e40282c + name: "Eric_mac\xEDas" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - hgv_david + - trim_galore + - fasterq_dump + - salmon + - tp_cut_tool + - tp_tail_tool + - tp_head_tool + - limma_voom + - gprofiler_gost + - tp_awk_tool + - deseq2 + - Filter1 + update_time: '2022-03-21' + versions: 8 +- create_time: '2022-03-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 43c39bc86399188f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=43c39bc86399188f + name: "Workflow constructed from history 'RNA-seq analysis Sandra Oz\xE1ez'" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - table_compute + - collection_column_join + - filter_tabular + - hgv_david + - tp_replace_in_line + - csv_to_tabular + - trim_galore + - fasterq_dump + - salmon + - tp_cut_tool + - tp_tail_tool + - tp_sed_tool + - limma_voom + - Filter1 + update_time: '2022-03-21' + versions: 0 +- create_time: '2022-03-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 5203bc68df3cf819 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=5203bc68df3cf819 + name: GeneAnalysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - hgv_david + - trim_galore + - fasterq_dump + - salmon + - tp_cut_tool + - tp_sed_tool + - tp_tail_tool + - tp_head_tool + - limma_voom + - tp_multijoin_tool + - Filter1 + update_time: '2022-03-20' + versions: 3 +- create_time: '2022-03-20' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + - Data handling + edam_topic: [] + id: 0c052e50594f6d2d + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0c052e50594f6d2d + name: Workflow constructed from history 'GeneExpressionAnalysis' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - hgv_david + - fasterq_dump + - tp_sed_tool + - tp_cut_tool + - tp_tail_tool + - tp_head_tool + - limma_voom + - Filter1 + update_time: '2022-03-20' + versions: 0 +- create_time: '2022-03-19' + creators: [] + doi: '' + edam_operation: + - Formatting + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Read mapping + - Variant calling + - Generation + - Sequence alignment + edam_topic: [] + id: feeec17310351914 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=feeec17310351914 + name: Identification of Polymorphism + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2022-03-19' + versions: 0 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 6c2bb2209aad5e44 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6c2bb2209aad5e44 + name: 'COVID-19: variation analysis reporting (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: dcbc71347300822d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=dcbc71347300822d + name: 'COVID-19: variation analysis reporting (release v0.1.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 2dceaa255cc8cf83 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2dceaa255cc8cf83 + name: 'COVID-19: variation analysis reporting (release v0.1.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: ff3ade25b35f4893 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893 + name: 'COVID-19: variation analysis reporting (release v0.1.3)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 7af656b8ea5e7e2e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=7af656b8ea5e7e2e + name: 'COVID-19: variation analysis reporting (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 5a0eb1b27dad3cd6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5a0eb1b27dad3cd6 + name: Parallel Accession Down (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 4f20cfc9589d7b2d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4f20cfc9589d7b2d + name: Parallel Accession Down (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: c41272bceb3292d8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c41272bceb3292d8 + name: Parallel Accession Down (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: db01ac5b0dc50cd4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=db01ac5b0dc50cd4 + name: 'COVID-19: variation analysis on WGS SE (release v0.1.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 53dda64a5a6ebd54 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=53dda64a5a6ebd54 + name: 'COVID-19: variation analysis on WGS SE (release v0.1.3)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 10c2136973c88d8a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=10c2136973c88d8a + name: 'COVID-19: variation analysis on WGS PE (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 26b35874b9e32355 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=26b35874b9e32355 + name: 'COVID-19: variation analysis on WGS PE (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5b3e2ddf525da25d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=5b3e2ddf525da25d + name: 'COVID-19: variation analysis on WGS PE (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bbe6f5a45ea5ee5e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bbe6f5a45ea5ee5e + name: 'COVID-19: variation analysis on WGS PE (release v0.2.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6b11d738ee57f245 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6b11d738ee57f245 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bd355e8ce58a139e + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bd355e8ce58a139e + name: 'COVID-19: variation analysis on ARTIC PE (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e282f505ba9f729f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=e282f505ba9f729f + name: 'COVID-19: variation analysis on ARTIC PE (release v0.3)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bf3ccae8d5b6ef58 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=bf3ccae8d5b6ef58 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4cf8cc42e97b2da6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4cf8cc42e97b2da6 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 98b2ac8fc75781f8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=98b2ac8fc75781f8 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - Pairwise sequence alignment + - SNP detection + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: d3428dd172a78102 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=d3428dd172a78102 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - lofreq_filter + - tp_find_and_replace + - minimap2 + - samtools_view + - snpeff_sars_cov_2 + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - SNP detection + - Pairwise sequence alignment + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: c12e6b7896f8e114 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c12e6b7896f8e114 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - snpeff_sars_cov_2 + - lofreq_filter + - minimap2 + - samtools_view + - tp_find_and_replace + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - SNP detection + - Pairwise sequence alignment + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 9adf8691809326e5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=9adf8691809326e5 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - snpeff_sars_cov_2 + - lofreq_filter + - minimap2 + - samtools_view + - tp_find_and_replace + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 4357180d40560019 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=4357180d40560019 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.3)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: c7b2d2ccc4b0dec5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=c7b2d2ccc4b0dec5 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.3.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 65f3a5772ae05a7a + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a + name: 'COVID-19: consensus construction (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 6ba03802169c0063 + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=6ba03802169c0063 + name: 'COVID-19: consensus construction (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 507c817755b2410d + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=507c817755b2410d + name: 'COVID-19: consensus construction (release v0.2.2)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 0392de36b6f55a8f + latest_version: 1 + license: MIT + link: https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f + name: 'COVID-19: consensus construction (release v0.3)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 95db417c58c586fa + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=95db417c58c586fa + name: Workflow constructed from history '2nd galaxy tutorial' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2022-03-18' + versions: 0 +- create_time: '2022-03-15' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 00a501a1fada4104 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=00a501a1fada4104 + name: Workflow constructed from history 'RNA-seq' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - multiqc + - featurecounts + - hisat2 + update_time: '2022-03-15' + versions: 0 +- create_time: '2022-02-23' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Formatting + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: bf90f2bd20fbff21 + latest_version: 20 + license: null + link: https://usegalaxy.org/published/workflow?id=bf90f2bd20fbff21 + name: NGS_Workflow_workshop + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_SortSam + - varscan_mpileup + - samtools_rmdup + - ivar_variants + - samtools_mpileup + - bowtie2 + - freebayes + update_time: '2022-03-15' + versions: 20 +- create_time: '2022-03-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7942748c29d718f8 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=7942748c29d718f8 + name: Workflow constructed from 'overlapping genes' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_intersect_1 + - cat_multiple + - Filter1 + update_time: '2022-03-14' + versions: 1 +- create_time: '2022-03-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 27e1a8c651d9a298 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=27e1a8c651d9a298 + name: Workflow 'overlapping genes features chr22' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_concat_1 + - gops_intersect_1 + - Filter1 + update_time: '2022-03-14' + versions: 1 +- create_time: '2022-03-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequence annotation + - Sequencing quality control + edam_topic: [] + id: 4e6005819e57ed35 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=4e6005819e57ed35 + name: TH workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-03-11' + versions: 1 +- create_time: '2022-03-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequence annotation + - Sequencing quality control + edam_topic: [] + id: 7b19452fe35b8b17 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=7b19452fe35b8b17 + name: Infected Trial Sequencing + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2022-03-11' + versions: 5 +- create_time: '2022-01-12' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: 3c7349268d74c576 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=3c7349268d74c576 + name: 1.12.21 Clean early stop + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - seq_filter_by_id + - filter_by_fasta_ids + - fasta2tab + - tp_sed_tool + - 'EMBOSS: transeq101' + update_time: '2022-03-09' + versions: 2 +- create_time: '2022-01-31' + creators: [] + doi: '' + edam_operation: + - Formatting + - Statistical calculation + - Genome indexing + - Read mapping + - Variant calling + - Sequence contamination filtering + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 1f48b44fa22ac5fc + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=1f48b44fa22ac5fc + name: VA-direct SARS-CoV-2 (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastp + - ngsutils_bam_filter + - ivar_variants + - qualimap_bamqc + - ivar_consensus + - bamleftalign + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-07' + versions: 10 +- create_time: '2022-02-22' + creators: [] + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: 806ef8816168916f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=806ef8816168916f + name: NPDN 2022 DADA2 (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - dada2_makeSequenceTable + - dada2_seqCounts + - dada2_learnErrors + - dada2_filterAndTrim + - dada2_mergePairs + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2022-02-24' + versions: 0 +- create_time: '2022-02-20' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: c81ae10f59b3f600 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=c81ae10f59b3f600 + name: 'Find exons with the highest number of features ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2022-02-20' + versions: 3 +- create_time: '2021-12-28' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 2b09f3c9465ee054 + latest_version: 0 + license: MIT + link: https://usegalaxy.org/published/workflow?id=2b09f3c9465ee054 + name: 'COVID-19: variation analysis reporting (imported from uploaded file)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-01-31' + versions: 0 +- create_time: '2022-01-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Visualisation + - Genome assembly + - Sequence composition calculation + - Aggregation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: a67afbea4b2eb26b + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=a67afbea4b2eb26b + name: Salmonelle + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - quast + - unicycler + - ncbi_blastn_wrapper + update_time: '2022-01-28' + versions: 2 +- create_time: '2022-01-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e2d7b8a4e6c422a3 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e2d7b8a4e6c422a3 + name: Workflow 'Bioinformatics Assignment Data' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-26' + versions: 0 +- create_time: '2022-01-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3bed12ef73ba93bf + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=3bed12ef73ba93bf + name: Workflow constructed from history 'Bioinformatics Assignment Olunmilayo Ogunremi..' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff_download + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - snpEff + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-26' + versions: 0 +- create_time: '2020-05-07' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 839cac17365affb7 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=839cac17365affb7 + name: Rna-seq Proyect + number_of_steps: null + source: https://usegalaxy.org + tags: + - Rna + - Rnaseq + - Bioinformatics + tools: + - fastqc + - multiqc + - trimmomatic + - bowtie2 + update_time: '2022-01-26' + versions: 6 +- create_time: '2020-06-06' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Genome visualisation + - Read mapping + - Nucleic acid sequence analysis + edam_topic: [] + id: ce232859a466c75c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ce232859a466c75c + name: Workflow constructed from history 'Rna-seq Data analisys' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - tabular_to_csv + - jbrowse + - htseq_count + - edger + - bowtie2 + update_time: '2022-01-26' + versions: 0 +- create_time: '2022-01-05' + creators: [] + doi: '' + edam_operation: + - Formatting + - Data handling + - Genome indexing + - Sequence file editing + - Read mapping + - Primer removal + - Sequence contamination filtering + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 35c2626849348f2c + latest_version: 47 + license: null + link: https://usegalaxy.org/published/workflow?id=35c2626849348f2c + name: Nameworkflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_fastx + - fastp + - bam_to_sam + - bwa + - cutadapt + - seqtk_mergepe + - samtools_view + - picard_MarkDuplicates + - cd_hit_dup + update_time: '2022-01-25' + versions: 47 +- create_time: '2016-06-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9b4323b68f609e06 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=9b4323b68f609e06 + name: Variant calling on Mother-Father-daughter trio + number_of_steps: null + source: https://usegalaxy.org + tags: + - Assingment + tools: + - fastqc + - sort1 + - vcfselectsamples + - bwa_mem + - Grouping1 + - cat1 + - table_annovar + - vcffilter2 + - fastq_groomer + - freebayes + update_time: '2022-01-19' + versions: 1 +- create_time: '2022-01-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ddb737f2ad0589e8 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8 + name: RNASeq Single End Pipeline + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - join1 + - salmon + - tp_cut_tool + - tp_tail_tool + - column_order_header_sort + - __RELABEL_FROM_FILE__ + - gprofiler_gost + - tp_find_and_replace + - Filter1 + - melt + - limma_voom + update_time: '2022-01-18' + versions: 2 +- create_time: '2022-01-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 76b8ed1c68678b62 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=76b8ed1c68678b62 + name: Tutorial Reference-based RNA-Seq data analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + - rseqc_infer_experiment + - rna_star + - multiqc + update_time: '2022-01-16' + versions: 2 +- create_time: '2022-01-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 22f6b939e97d3b47 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=22f6b939e97d3b47 + name: Bioinformatics_assignment_2021 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-12' + versions: 0 +- create_time: '2022-01-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d85f8ef78040fbb1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d85f8ef78040fbb1 + name: Workflow constructed from history 'WES01 NGS Workshop - BOH m2108139' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-10' + versions: 0 +- create_time: '2022-01-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bb16936081b820f6 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=bb16936081b820f6 + name: Workflow constructed from history 'original Data Handling Assessment' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - snpSift_extractFields + - picard_AddOrReplaceReadGroups + - vcf2tsv + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - samtools_idxstats + - bam_to_sam + - sort1 + - vcfsort + - table_annovar + - samtools_flagstat + - snpEff + - samtool_filter2 + - freebayes + - bwa_mem + - Filter1 + - lofreq_call + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2022-01-10' + versions: 0 +- create_time: '2022-01-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bfee1238c70627cb + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=bfee1238c70627cb + name: Workflow constructed from history 'VariantAnalysisPipeline' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-10' + versions: 0 +- create_time: '2022-01-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e6b803c1232cd08e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e6b803c1232cd08e + name: Workflow constructed from history 'NGS_VariantAnalysis' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-10' + versions: 0 +- create_time: '2022-01-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ec96e3bf30d5f771 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ec96e3bf30d5f771 + name: Alignment_variant_calling_and_filtering-v0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-08' + versions: 0 +- create_time: '2022-01-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 50206b10de958d03 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=50206b10de958d03 + name: Data Handling Assessment-2022 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - snpSift_extractFields + - vcf2tsv + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - samtools_idxstats + - bam_to_sam + - sort1 + - vcfsort + - table_annovar + - samtools_flagstat + - snpEff + - samtool_filter2 + - freebayes + - bwa_mem + - Filter1 + - lofreq_call + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2022-01-04' + versions: 0 +- create_time: '2022-01-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: fae519dcba6bfc72 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72 + name: Data Handling Assessment + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - snpSift_extractFields + - vcf2tsv + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - samtools_idxstats + - bam_to_sam + - sort1 + - vcfsort + - table_annovar + - samtools_flagstat + - snpEff + - samtool_filter2 + - freebayes + - bwa_mem + - Filter1 + - lofreq_call + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2022-01-04' + versions: 0 +- create_time: '2022-01-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ab8590a0ee1b9951 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ab8590a0ee1b9951 + name: Workflow constructed from history 'Seher Keskin- m2108649- Bioinformatics + Assignment' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-03' + versions: 0 +- create_time: '2022-01-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0660a00407fc16a1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0660a00407fc16a1 + name: Workflow constructed from history 'Diana Alakhmad,M2007005,Bioinformatics + assessment history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2022-01-03' + versions: 0 +- create_time: '2021-12-25' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: dfa8c64634aec75c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=dfa8c64634aec75c + name: sonnn + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastp + - snpSift_extractFields + - bcftools_view + - lofreq_call + - lofreq_indelqual + - snpEff_download + - snpEff + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2021-12-25' + versions: 0 +- create_time: '2021-12-23' + creators: + - The Vera-Licona Research Group + - Lauren Marazzi + - Shreedula Balakrishnan + doi: '' + edam_operation: [] + edam_topic: [] + id: 661017a43a71d5df + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=661017a43a71d5df + name: NETISCE + number_of_steps: null + source: https://usegalaxy.org + tags: + - systemsbiology + - networkanalysis + tools: + - netisce12 + - netisce10 + - netisce3 + - netisce7 + - netisce9 + - netisce5 + - netisce2 + - netisce8 + - netisce11 + - netisce13 + - netisce4 + - netisce6 + - netisce1 + update_time: '2021-12-23' + versions: 1 +- create_time: '2021-12-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b33ad2032a655706 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b33ad2032a655706 + name: Bioinformatics_Assignment_Shahid_Bashir + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - samtools_idxstats + - bam_to_sam + - bcftools_stats + - sort1 + - snpEff_databases + - snpEff_download + - CONVERTER_bam_to_coodinate_sorted_bam + - CONVERTER_bam_to_bigwig_0 + - table_annovar + - samtools_flagstat + - snpEff + - CONVERTER_interval_to_bedstrict_0 + - samtool_filter2 + - freebayes + - bwa_mem + - Filter1 + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2021-12-22' + versions: 0 +- create_time: '2021-11-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 60b080dc16141121 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=60b080dc16141121 + name: Workflow constructed from history 'Intro - Strands (LV)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_cat + - gops_intersect_1 + - Filter1 + update_time: '2021-12-16' + versions: 0 +- create_time: '2021-12-13' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Sequence trimming + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 58a7a02dade085cf + latest_version: 19 + license: null + link: https://usegalaxy.org/published/workflow?id=58a7a02dade085cf + name: miRNA adapter remove + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastp + - cshl_fastq_quality_filter + - cutadapt + - cshl_fastx_reverse_complement + update_time: '2021-12-13' + versions: 19 +- create_time: '2021-12-08' + creators: [] + doi: '' + edam_operation: + - RNA-Seq quantification + - Gene expression profiling + - Gene expression analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - RNA-Seq analysis + - Transcriptome assembly + - Generation + - Sequence alignment + edam_topic: [] + id: c2c6779a8b1821e0 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0 + name: Benchmarking RNA-seq Cloud Costs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - stringtie + - salmon + - fastq_paired_end_deinterlacer + - kallisto_quant + - bowtie2 + - bwa_mem + update_time: '2021-12-08' + versions: 1 +- create_time: '2021-12-08' + creators: [] + doi: '' + edam_operation: + - RNA-Seq quantification + - Gene expression profiling + - Gene expression analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - RNA-Seq analysis + - Transcriptome assembly + - Generation + - Sequence alignment + edam_topic: [] + id: 08bdcecd1cb0bda3 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=08bdcecd1cb0bda3 + name: Benchmarking RNA Single-Read Cloud Costs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - stringtie + - salmon + - kallisto_quant + - bowtie2 + - bwa_mem + update_time: '2021-12-08' + versions: 1 +- create_time: '2021-12-03' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - Transcriptome assembly + - Data handling + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b77fa73d4fbde131 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b77fa73d4fbde131 + name: Workflow constructed from history 'Copy of 'RNA Seq SARS-COV-2' (2)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - deg_annotate + - trimmomatic + - stringtie + - fastq_dump + - stringtie_merge + - deseq2 + - hisat2 + update_time: '2021-12-07' + versions: 0 +- create_time: '2020-12-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 07fdeadce7a6d5cb + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb + name: RNASeq CEU + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - gffread + - Cut1 + - trim_galore + - fasterq_dump + - salmon + - tp_cut_tool + - tp_tail_tool + - __RELABEL_FROM_FILE__ + - limma_voom + update_time: '2021-12-01' + versions: 4 +- create_time: '2020-10-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Genome assembly + - Sequence composition calculation + - Multilocus sequence typing + - Coding region prediction + - Genome annotation + - Visualisation + - Antimicrobial resistance prediction + - Gene prediction + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fb01e1a49793c8be + latest_version: 16 + license: null + link: https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be + name: BIOL4802 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - kraken + - abricate + - trimmomatic + - quast + - spades + - mlst + - prokka + - kraken-report + - bandage_image + update_time: '2021-11-29' + versions: 16 +- create_time: '2021-11-09' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 2d50f038984f2389 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2d50f038984f2389 + name: Workflow constructed from history 'Galaxy 101_Katya' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2021-11-09' + versions: 1 +- create_time: '2021-11-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b4f7109ac83ce199 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=b4f7109ac83ce199 + name: SPRING Map Cross-Reference-alam + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - spring_map + - split_file_to_collection + - collapse_dataset + update_time: '2021-11-04' + versions: 1 +- create_time: '2021-10-20' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 9aa6320de30e2675 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=9aa6320de30e2675 + name: Exploring Iris dataset with statistics and scatterplots-khairul + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:test + tools: + - sort1 + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - ggplot2_point + update_time: '2021-11-03' + versions: 6 +- create_time: '2021-07-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e133a816f99ba43d + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=e133a816f99ba43d + name: Convert Newick for branchify + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sed_tool + update_time: '2021-11-03' + versions: 3 +- create_time: '2021-11-01' + creators: [] + doi: '' + edam_operation: + - Multilocus sequence typing + edam_topic: [] + id: 675d70ee099dd3f2 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=675d70ee099dd3f2 + name: Download list of isolates & type + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - ncbi_acc_download + - mlst + update_time: '2021-11-01' + versions: 3 +- create_time: '2021-10-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7cff5c4dadffaad5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=7cff5c4dadffaad5 + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_cluster_1 + update_time: '2021-10-26' + versions: 0 +- create_time: '2021-10-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ebac500f62f4a469 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=ebac500f62f4a469 + name: From peaks to genes + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:suhasini + tools: + - Grouping1 + - gops_intersect_1 + update_time: '2021-10-22' + versions: 2 +- create_time: '2021-10-18' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: cb029d0205155150 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=cb029d0205155150 + name: Find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:suhasini + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2021-10-22' + versions: 2 +- create_time: '2021-10-19' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 987d5caea37794c8 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=987d5caea37794c8 + name: Exploring Iris datasets with statistics and scatterplots + number_of_steps: null + source: https://usegalaxy.org + tags: + - name:suhasini + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2021-10-22' + versions: 3 +- create_time: '2021-10-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5641d1cbe795203f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5641d1cbe795203f + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bamFilter + - bwa + - qualimap_bamqc + - cshl_fastx_trimmer + - bamleftalign + - picard_MarkDuplicates + - bcftools_plugin_counts + - freebayes + update_time: '2021-10-19' + versions: 0 +- create_time: '2021-10-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 044c5ce43f2e1829 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829 + name: Workflow constructed from history 'RNAseq' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - gtftobed12 + - samtools_idxstats + - rseqc_read_distribution + - rseqc_geneBody_coverage + - cutadapt + - rseqc_infer_experiment + - rna_star + - multiqc + - picard_MarkDuplicates + - featurecounts + update_time: '2021-10-18' + versions: 0 +- create_time: '2021-10-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 888bfce1c214ab64 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=888bfce1c214ab64 + name: From peak to genes + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - get_flanks1 + - CONVERTER_interval_to_bed_0 + - gops_intersect_1 + - Grouping1 + - tp_tail_tool + - tp_replace_in_column + update_time: '2021-10-18' + versions: 0 +- create_time: '2021-10-18' + creators: + - null + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Taxonomic classification + - Genome indexing + - Sequence composition calculation + - Read mapping + - Visualisation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b68ec42db8953569 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b68ec42db8953569 + name: Metatranscriptomics - analyze human RNA-seq data with Kraken (imported from + uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: + - metatranscriptomics + - Kraken + - RNA-seq + - microbiome + tools: + - fastqc + - Kraken2Tax + - trimmomatic + - taxonomy_krona_chart + - bwa + - kraken2 + - picard_SamToFastq + - samtools_view + update_time: '2021-10-18' + versions: 0 +- create_time: '2021-10-16' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 4e8639cc4e9050d1 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=4e8639cc4e9050d1 + name: Galaxy 101 Bioinformatics Tutorial- Finding the exon with the highest number + SNPs in human Chromosome 22 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - tp_head_tool + - comp1 + update_time: '2021-10-16' + versions: 1 +- create_time: '2021-10-11' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: ce4d4397eb8a5298 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ce4d4397eb8a5298 + name: Exploring Iris dataset with statistics and scatterplots + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - csv_to_tabular + - datamash_ops + - tp_cut_tool + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2021-10-11' + versions: 0 +- create_time: '2021-10-09' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 2cfbf7d01161992c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=2cfbf7d01161992c + name: Find axons with the highest number of features + number_of_steps: null + source: https://usegalaxy.org + tags: + - Genome + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2021-10-09' + versions: 2 +- create_time: '2021-09-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6cb8b40b819f2764 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=6cb8b40b819f2764 + name: Workflow constructed from history 'TEST galaxy PM' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2021-09-30' + versions: 0 +- create_time: '2021-09-29' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: 0e3e3958f55c606e + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=0e3e3958f55c606e + name: testing more + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - datamash_ops + - bcftools_norm + - compose_text_param + - param_value_from_file + - bowtie2 + update_time: '2021-09-30' + versions: 2 +- create_time: '2021-04-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f85999e42bfef5b9 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=f85999e42bfef5b9 + name: SPRING Map Cross-Reference + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - spring_map + - split_file_to_collection + - collapse_dataset + update_time: '2021-09-29' + versions: 2 +- create_time: '2021-09-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5324757bc3974635 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5324757bc3974635 + name: Storytime_Demo + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - tp_head_tool + update_time: '2021-09-28' + versions: 1 +- create_time: '2021-09-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e035be74e3c85bf5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e035be74e3c85bf5 + name: Workflow constructed from history 'Reference-based RNA-Seq data analysis' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + - rseqc_infer_experiment + - rna_star + - multiqc + update_time: '2021-09-25' + versions: 0 +- create_time: '2021-09-24' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Mapping + - Read mapping + - Sequence alignment + edam_topic: [] + id: 6be2c7930c391b35 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=6be2c7930c391b35 + name: Mapping, Variant Calling, and Get draft genome Fasta + number_of_steps: null + source: https://usegalaxy.org + tags: + - Fasta + - NGS + - Genome + - Draft + tools: + - bedtools_mergebed + - snpSift_extractFields + - bedtools_bamtobed + - lofreq_call + - snpEff_build_gb + - snpEff + - bedtools_getfastabed + - bcftools_consensus + - bwa_mem + update_time: '2021-09-24' + versions: 7 +- create_time: '2021-09-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 35209d092e636cd8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=35209d092e636cd8 + name: RNA seq-analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - deg_annotate + - trimmomatic + - stringtie + - hisat2 + update_time: '2021-09-20' + versions: 0 +- create_time: '2020-12-17' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Sequence analysis + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - Multiple sequence alignment + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: 603e5c61c57bcf3f + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f + name: Phylogenetic analysis Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: + - phylogeny + - fasta + - phylogenetic + tools: + - mothur_fastq_info + - rbc_mafft + - clustalw + - newick_display + - iqtree + update_time: '2021-09-07' + versions: 4 +- create_time: '2021-09-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 1dd60e57d1d00406 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=1dd60e57d1d00406 + name: Workflow constructed from history 'Genomic DS Capstone' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - featurecounts + - hisat2 + update_time: '2021-09-07' + versions: 0 +- create_time: '2021-09-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Visualisation + - Genome assembly + - Sequence composition calculation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: db08887d7d6dc147 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=db08887d7d6dc147 + name: Workflow constructed from history 'Firefly mitogenome' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - shovill + - trimmomatic + - quast + update_time: '2021-09-05' + versions: 0 +- create_time: '2021-09-02' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: 52a2cca52985cdc7 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=52a2cca52985cdc7 + name: 'RNA-seq ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffcompare + - cufflinks + - cuffdiff + - cuffmerge + - bowtie2 + update_time: '2021-09-02' + versions: 3 +- create_time: '2021-08-09' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + edam_topic: [] + id: b04989efde68dee2 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=b04989efde68dee2 + name: 20210810 preprocessing for DESeq2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - featurecounts + - hisat2 + update_time: '2021-09-02' + versions: 5 +- create_time: '2021-08-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2b1c98865a3ce11a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2b1c98865a3ce11a + name: DEG:Tuxedo2 - 2 Conditions 3 Replicates each + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffcompare + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + update_time: '2021-08-17' + versions: 1 +- create_time: '2021-08-16' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Data handling + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 6da54816b436dc58 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=6da54816b436dc58 + name: Variant calling workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_dump + - vcfbedintersect + - bowtie2 + - createInterval + - freebayes + update_time: '2021-08-16' + versions: 2 +- create_time: '2021-08-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c828990fb009e318 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c828990fb009e318 + name: Workflow constructed from history 'Stage2 Analyze data of polymorphic sites + based on VCF file Protocol' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Grouping1 + - bcftools_stats + - table_annovar + - vcffilter2 + - bcftools_plugin_counts + update_time: '2021-08-13' + versions: 0 +- create_time: '2021-08-12' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Sequence contamination filtering + - Formatting + - Statistical calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: b300d028da9b8396 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b300d028da9b8396 + name: Workflow constructed from history 'Stage1 Variant Analysis of pair end Illumina + reads Collection' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastp + - picard_MergeSamFiles + - picard_CleanSam + - picard_AddOrReplaceReadGroups + - samtools_view + - vcffilter2 + - freebayes + - hisat2 + update_time: '2021-08-13' + versions: 0 +- create_time: '2021-08-10' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Data handling + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3f92474cd16ca314 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=3f92474cd16ca314 + name: Workflow constructed from history 'NGS_Management' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastp + - fasterq_dump + - tp_cut_tool + - Grep1 + - bwa_mem + update_time: '2021-08-10' + versions: 0 +- create_time: '2021-06-10' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: ea3257e0ef9f505a + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=ea3257e0ef9f505a + name: Workflow constructed from history 'Clustering 3K PBMCs with Scanpy' + number_of_steps: null + source: https://usegalaxy.org + tags: + - Single_Cell + - Scanpy + tools: + - anndata_manipulate + - scanpy_filter + - anndata_inspect + - Cut1 + - tp_cat + - scanpy_inspect + - scanpy_cluster_reduce_dimension + - scanpy_normalize + - tp_replace_in_column + - tp_tail_tool + - tp_awk_tool + - scanpy_plot + - scanpy_remove_confounders + - anndata_import + - Filter1 + update_time: '2021-06-21' + versions: 4 +- create_time: '2021-05-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e51aaf4d6b16b4d4 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e51aaf4d6b16b4d4 + name: Trio_FamilyAnalysis_NAvsHG19_SNPs_MNPs_INDELs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - bcftools_stats + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2021-05-30' + versions: 1 +- create_time: '2021-05-12' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 2d149545a4920326 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=2d149545a4920326 + name: Workflow constructed from history 'workflow for me' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_remove_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_unique_seqs + - mothur_align_seqs + - mothur_classify_seqs + - mothur_pre_cluster + update_time: '2021-05-12' + versions: 0 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 58ce6470337a190d + latest_version: 14 + license: null + link: https://usegalaxy.org/published/workflow?id=58ce6470337a190d + name: WSP 1-Miao Lu + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - Filter1 + update_time: '2021-05-07' + versions: 14 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 17beb47e45a7690c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=17beb47e45a7690c + name: workshop1 workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + update_time: '2021-05-07' + versions: 1 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 794e7e952003d3d9 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=794e7e952003d3d9 + name: BINF6000 workflow1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + update_time: '2021-05-06' + versions: 5 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: acec9c2c67fcaf13 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=acec9c2c67fcaf13 + name: Cuffdiff + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffdiff + - Filter1 + update_time: '2021-05-06' + versions: 4 +- create_time: '2021-05-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b23c3db251eca105 + latest_version: 23 + license: null + link: https://usegalaxy.org/published/workflow?id=b23c3db251eca105 + name: Workshop1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffdiff + update_time: '2021-05-06' + versions: 23 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 2566f7c6bef19b18 + latest_version: 16 + license: null + link: https://usegalaxy.org/published/workflow?id=2566f7c6bef19b18 + name: Analysis of differentially expressed genes + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - Filter1 + update_time: '2021-05-06' + versions: 16 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fa9cb11930ef8297 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=fa9cb11930ef8297 + name: BINF6000 workshop 1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffdiff + - Filter1 + update_time: '2021-05-06' + versions: 0 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: e7bfa3c733835b22 + latest_version: 16 + license: null + link: https://usegalaxy.org/published/workflow?id=e7bfa3c733835b22 + name: gene expression + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - Filter1 + update_time: '2021-05-06' + versions: 16 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 87fab09e4c592435 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=87fab09e4c592435 + name: Workflow constructed from history 'BINF6000' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cufflinks + - cuffdiff + - tophat2 + - cutadapt + - cuffmerge + - Filter1 + update_time: '2021-05-06' + versions: 1 +- create_time: '2021-05-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 07e4414905458c86 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=07e4414905458c86 + name: Workflow - 'BINF' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cufflinks + - cuffdiff + - tophat2 + - cutadapt + - cuffmerge + - Filter1 + update_time: '2021-05-06' + versions: 1 +- create_time: '2021-05-05' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + edam_topic: [] + id: bdbfd1206c59469a + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=bdbfd1206c59469a + name: Haiming Li_BINF 6000_workshop 1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Filter1 + - cuffdiff + - hisat2 + update_time: '2021-05-06' + versions: 3 +- create_time: '2021-05-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a0503b2ea964127b + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=a0503b2ea964127b + name: BINF6000 workshop 1- performing the differential gene analysis using the CuffDiff + tool + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffdiff + update_time: '2021-05-05' + versions: 2 +- create_time: '2021-05-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b5ac201b63a32a9b + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=b5ac201b63a32a9b + name: Workflow constructed from history 'Mazen Ali' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffdiff + - Filter1 + update_time: '2021-05-05' + versions: 4 +- create_time: '2021-05-04' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Nucleic acid sequence analysis + - RNA-Seq quantification + edam_topic: [] + id: 41c09a87c6cd5f75 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=41c09a87c6cd5f75 + name: Workshop1 Galaxy website + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffdiff + - tp_multijoin_tool + - featurecounts + - htseq_count + update_time: '2021-05-04' + versions: 0 +- create_time: '2019-11-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7003470003f4a57b + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=7003470003f4a57b + name: Find exons with highest SNPs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - tp_head_tool + - comp1 + update_time: '2021-04-28' + versions: 1 +- create_time: '2021-02-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Genome assembly + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: ae81cc0e8263d03e + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e + name: Quality Control + number_of_steps: null + source: https://usegalaxy.org + tags: + - Workflow + - test + tools: + - fastqc + - trimmomatic + - spades + - fastq_dump + - fastq_paired_end_deinterlacer + update_time: '2021-04-22' + versions: 2 +- create_time: '2021-04-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 292b9d1975c349f3 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=292b9d1975c349f3 + name: Find exons with the highest number of SNPs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2021-04-08' + versions: 1 +- create_time: '2021-04-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9c0bbf9e1c90cd66 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=9c0bbf9e1c90cd66 + name: Workflow constructed from history 'Coursera galaxy final assignment E Grajales + Esquivel + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2021-04-06' + versions: 0 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 80afe572b6693ca1 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=80afe572b6693ca1 + name: 'NrD Workflow: 8 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2021-04-01' + versions: 5 +- create_time: '2021-01-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Genome assembly + - Sequence composition calculation + - Coding region prediction + - Sequence analysis + - Genome annotation + - Gene prediction + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 33d90e718ce500ef + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=33d90e718ce500ef + name: metagenomics + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - kraken + - cat_bins + - trimmomatic + - PlasFlow + - cat_contigs + - prokka + - kraken-report + - metaspades + - cat_prepare + - maxbin2 + update_time: '2021-03-31' + versions: 10 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 66bc5f6d71466b7f + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=66bc5f6d71466b7f + name: 'NrD Workflow: 2 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2021-03-31' + versions: 6 +- create_time: '2021-03-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Multilocus sequence typing + - Aggregation + - Coding region prediction + - Genome annotation + - Visualisation + - Antimicrobial resistance prediction + - Gene prediction + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 8111bb9bb26bb665 + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665 + name: Bacterial genome paired-end assembly using Unicycler + number_of_steps: null + source: https://usegalaxy.org + tags: + - assembly + - pe + - unicycler + - wgs + tools: + - fastqc + - abricate + - quast + - bandage_info + - unicycler + - mlst + - prokka + - bandage_image + update_time: '2021-03-30' + versions: 11 +- create_time: '2021-03-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Multilocus sequence typing + - Aggregation + - Coding region prediction + - Genome annotation + - Visualisation + - Antimicrobial resistance prediction + - Gene prediction + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: c65bec6c332bf740 + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=c65bec6c332bf740 + name: Bacterial genome hybrid assembly using Unicycler + number_of_steps: null + source: https://usegalaxy.org + tags: + - assembly + - unicycler + - hybrid + - wgs + tools: + - fastqc + - abricate + - quast + - bandage_info + - unicycler + - mlst + - prokka + - bandage_image + update_time: '2021-03-30' + versions: 9 +- create_time: '2020-07-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0f43ad9dfd0f6d16 + latest_version: 51 + license: null + link: https://usegalaxy.org/published/workflow?id=0f43ad9dfd0f6d16 + name: Baculovirus internal SNP Variant ( NGS, illumina data) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bcftools_call + - trim_galore + - vcffilter2 + - samtools_mpileup + - bwa_mem + update_time: '2021-03-26' + versions: 51 +- create_time: '2019-09-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Primer removal + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: d5514e327878b531 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=d5514e327878b531 + name: RNASeqAnalysisFromSRATwoSamples + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - trim_galore + - tp_cut_tool + - tp_tail_tool + - fastq_dump + - limma_voom + - htseq_count + - hisat2 + update_time: '2021-03-23' + versions: 4 +- create_time: '2021-03-18' + creators: + - Sneider Gutierrez Guarnizo + doi: '' + edam_operation: + - Formatting + - Statistical calculation + - Genome indexing + - Read mapping + - Primer removal + - Variant calling + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + edam_topic: [] + id: 7020413598cc2023 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=7020413598cc2023 + name: Variant_Calling_Analysis_comparing_2_groups_of_paired_reads_bySGG + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + - Trimming + - BWA-MEM + - SortSAM + - MarkDuplicates + - BamCoverage + - FreeBayes + - VCFfilter + - Bcftools + tools: + - picard_SortSam + - snpSift_extractFields + - deeptools_bam_coverage + - trim_galore + - vcffilter2 + - bcftools_stats + - bcftools_plugin_color_chrs + - snpEff + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2021-03-18' + versions: 5 +- create_time: '2021-03-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Read pre-processing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 623dcf47f7963700 + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=623dcf47f7963700 + name: Workflow constructed from history 'ZARSA708 (Part I)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bowtie2 + - trim_galore + update_time: '2021-03-16' + versions: 13 +- create_time: '2021-03-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Read pre-processing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 7ee7412cdd82f1ee + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=7ee7412cdd82f1ee + name: Workflow constructed from history 'b' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bowtie2 + - trim_galore + update_time: '2021-03-16' + versions: 3 +- create_time: '2021-03-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: bc461addefad698a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=bc461addefad698a + name: Find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2021-03-15' + versions: 1 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 49ca77212cc56ef9 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=49ca77212cc56ef9 + name: 'NrD Workflow: 3 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2021-03-11' + versions: 4 +- create_time: '2021-03-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8e5efd04399c6838 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8e5efd04399c6838 + name: From peaks to genes (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - CONVERTER_interval_to_bed_0 + - gops_intersect_1 + update_time: '2021-03-11' + versions: 0 +- create_time: '2015-11-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c74a01ba2f2a80d3 + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=c74a01ba2f2a80d3 + name: 'NrD Workflow: 4 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2021-03-09' + versions: 13 +- create_time: '2021-03-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 725f7ffa1cffa069 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=725f7ffa1cffa069 + name: Workflow constructed from history 'Copy of 'Snv'' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - freebayes + - bwa_mem + update_time: '2021-03-07' + versions: 0 +- create_time: '2021-02-23' + creators: + - Julie Zaworski + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Read pre-processing + - Read summarisation + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: e04f443a8ceca0d2 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=e04f443a8ceca0d2 + name: RNAseq_pairedend_trim_map_counts_merge_JZ + number_of_steps: null + source: https://usegalaxy.org + tags: + - rnaseq + - paired-end + - prokaryotes + - bowtie2 + - htseq + - featurecounts + - collections + tools: + - fastqc + - collection_column_join + - trim_galore + - samtools_stats + - htseq_count + - samtools_flagstat + - bowtie2 + - featurecounts + update_time: '2021-03-01' + versions: 5 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - Pairwise sequence alignment + - SNP detection + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 88d0b64011c3148c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=88d0b64011c3148c + name: 'COVID-19: variation analysis of ARTIC ONT data' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - lofreq_filter + - tp_find_and_replace + - minimap2 + - samtools_view + - snpeff_sars_cov_2 + - multiqc + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5a610d5a42d50cf3 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5a610d5a42d50cf3 + name: 'COVID-19: variation analysis on WGS PE data' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d4ea6cdd40522eb1 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=d4ea6cdd40522eb1 + name: 'COVID-19: variation analysis on ARTIC PE data' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: c092a3631d68ce38 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c092a3631d68ce38 + name: 'COVID-19: variation analysis on WGS SE data' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2967ef82911f2cca + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2967ef82911f2cca + name: 'COVID-19: variation analysis reporting' + number_of_steps: null + source: https://usegalaxy.org + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - tp_sort_header_tool + - tp_split_on_column + - datamash_ops + - tp_easyjoin_tool + - tp_tail_tool + - tp_head_tool + - cat1 + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: b2e81f82ccf3afd6 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b2e81f82ccf3afd6 + name: Workflow constructed from history 'Genomic Data Science Capstone' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - fastq_dump + - featurecounts + - hisat2 + update_time: '2021-02-03' + versions: 0 +- create_time: '2014-07-20' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Formatting + - Sequencing quality control + edam_topic: [] + id: c64719e91e7346a2 + latest_version: 54 + license: null + link: https://usegalaxy.org/published/workflow?id=c64719e91e7346a2 + name: RNAseqTRAPLINE + number_of_steps: null + source: https://usegalaxy.org + tags: + - rnaseq + - tophat2 + - fastq + - protein_interaction + - miRNA_target_prediction + - network_construction + - de_genes + - splice_variants + tools: + - fastqc + - hgv_david + - cuffdiff + - join1 + - fastq_quality_trimmer + - fastq_groomer + - cufflinks + - Grep1 + - Convert characters1 + - sort1 + - Add_a_column1 + - tophat2 + - comp1 + - Show beginning1 + - Filter1 + - cshl_fastx_clipper + - Cut1 + - cuffmerge + - picard_MarkDuplicates + update_time: '2021-01-28' + versions: 54 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 52cc435f50a6ff29 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=52cc435f50a6ff29 + name: 'NrD Workflow: 9 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2021-01-21' + versions: 5 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 74fe080f24f7da84 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=74fe080f24f7da84 + name: 'NrD Workflow: 6 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2021-01-21' + versions: 4 +- create_time: '2021-01-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 02755c14619242da + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=02755c14619242da + name: Workflow constructed from history 'Tom Basaran - Galaxy Assignment' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2021-01-21' + versions: 0 +- create_time: '2021-01-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2dd4f04c7de7d173 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=2dd4f04c7de7d173 + name: Alignment_Variant_Calling_and_Filtering-v0.1 UT + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2021-01-07' + versions: 0 +- create_time: '2021-01-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 17a7ff756d37a437 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=17a7ff756d37a437 + name: 'Workflow constructed from history ''Bioinformatics Assignment, Umelue Vincent, + candidate number: 18054''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - snpEff_download + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - snpEff + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2021-01-06' + versions: 0 +- create_time: '2021-01-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d7049965ca7d8ea9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d7049965ca7d8ea9 + name: Workflow constructed from history ''Bioinformatics2_AB05689'' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2021-01-05' + versions: 0 +- create_time: '2021-01-03' + creators: [] + doi: '' + edam_operation: + - Genome annotation + - Transcriptome assembly + - Genome assembly + - Sequence assembly validation + - Scaffolding + edam_topic: [] + id: 65b4051e722228b8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=65b4051e722228b8 + name: "Workflow constructed from history '\u57FA\u56E0\u6CE8\u91CA'" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasta-stats + - jcvi_gff_stats + - busco + - maker + update_time: '2021-01-03' + versions: 0 +- create_time: '2021-01-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 76247065c01f01d1 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=76247065c01f01d1 + name: ' NGS0001 BIOINFORMATICS ASSESSMENT WORKFLOW' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2021-01-03' + versions: 2 +- create_time: '2020-12-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Primer removal + - Sequence annotation + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6d0a3f36d2736087 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087 + name: 'First Workflow ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gffread + - collection_column_join + - Cut1 + - trim_galore + - fasterq_dump + - salmon + - tp_cut_tool + - tp_tail_tool + - column_order_header_sort + - Grep1 + - __RELABEL_FROM_FILE__ + - gprofiler_gost + - tp_find_and_replace + - Filter1 + - limma_voom + update_time: '2020-12-21' + versions: 4 +- create_time: '2020-12-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9f5f2e309a3ea50c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=9f5f2e309a3ea50c + name: alignment-variant-calling-filtering-v0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2020-12-15' + versions: 1 +- create_time: '2020-12-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3b49ba6b36b863f7 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=3b49ba6b36b863f7 + name: Exons and CpG Islands + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - join1 + - tp_cut_tool + update_time: '2020-12-11' + versions: 1 +- create_time: '2020-12-01' + creators: [] + doi: '' + edam_operation: + - Formatting + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0a57740c68e85e21 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0a57740c68e85e21 + name: Etapa 3 - Mapping / Variant Call - DNAnc-DNAmt (Update 01.12.20) (imported + from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sam_merge2 + - picard_FixMateInformation + - bedtools_genomecoveragebed + - gops_join_1 + - bamFilter + - bwa_mem + - fastq_paired_end_interlacer + - vcffilter2 + - qualimap_bamqc + - bcftools_norm + - bcftools_merge + - bamleftalign + - picard_MarkDuplicates + - Filter1 + - freebayes + - picard_ValidateSamFile + update_time: '2020-12-01' + versions: 0 +- create_time: '2020-12-01' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 947340358dd268ea + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=947340358dd268ea + name: Etapa 2 - Clean Up - (Update 21.07.19) (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + - trimmomatic + - cshl_fastx_artifacts_filter + update_time: '2020-12-01' + versions: 0 +- create_time: '2020-12-01' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: c446105e87750aa2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c446105e87750aa2 + name: "Etapa 1 - An\xE1lise de Qualidade - (Update 21.07.19) (imported from uploaded\ + \ file)" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_groomer + - fastq_paired_end_interlacer + update_time: '2020-12-01' + versions: 0 +- create_time: '2020-09-26' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + edam_topic: [] + id: 812bc1b7a52f4f6f + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=812bc1b7a52f4f6f + name: WT_20wk_AL + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - featurecounts + - hisat2 + update_time: '2020-11-17' + versions: 7 +- create_time: '2020-11-04' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: 94da3d448bb8a137 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=94da3d448bb8a137 + name: BMI 6030 Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - filter_by_fasta_ids + - 'EMBOSS: matcher52' + - rbc_splitfasta + update_time: '2020-11-10' + versions: 4 +- create_time: '2020-11-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5ce5b3061c6afd82 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=5ce5b3061c6afd82 + name: Workflow for CA! + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bwa + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2020-11-05' + versions: 2 +- create_time: '2020-11-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 71f129d96b81851e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=71f129d96b81851e + name: Copy of Workflow constructed from history 'Workflow constructed from history + 'CA'' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - vcffilter2 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2020-11-02' + versions: 0 +- create_time: '2020-07-07' + creators: [] + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a3c2ff6728c8c7a8 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a3c2ff6728c8c7a8 + name: Parallel accession download Illumina + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2020-10-07' + versions: 1 +- create_time: '2020-10-05' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: ae359a3c83f2e19f + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=ae359a3c83f2e19f + name: Workflow constructed from history 'variant_analysis' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bcftools_plugin_counts + - freebayes + - bwa_mem + update_time: '2020-10-06' + versions: 1 +- create_time: '2020-09-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: d97a88a8f9061e25 + latest_version: 37 + license: null + link: https://usegalaxy.org/published/workflow?id=d97a88a8f9061e25 + name: PPFinal-PE-091320 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2020-09-28' + versions: 37 +- create_time: '2020-09-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: e22ea88bc0fdc146 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=e22ea88bc0fdc146 + name: PPFinal-SE-091320 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - fastq_dump + - featurecounts + - hisat2 + update_time: '2020-09-23' + versions: 2 +- create_time: '2020-09-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 88ac2698fa170993 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=88ac2698fa170993 + name: Workflow constructed from history 'My Example -Aug 27,20' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - join1 + - Grouping1 + - tp_cut_tool + - Show beginning1 + update_time: '2020-09-03' + versions: 0 +- create_time: '2019-05-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Variant calling + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f1a9667c0b0999f4 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=f1a9667c0b0999f4 + name: TT52on&off + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - allele_counts_1 + - trim_galore + - samtools_rmdup + - naive_variant_caller + - bamleftalign + - samtools_flagstat + - bwa_mem + update_time: '2020-08-25' + versions: 4 +- create_time: '2020-07-30' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + edam_topic: [] + id: 0a009cf9e88171f1 + latest_version: 35 + license: null + link: https://usegalaxy.org/published/workflow?id=0a009cf9e88171f1 + name: RNASeq DE (5 Groups, 3 Replicates_2 Factors) (READ ANNOTATION) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + - DE + - Differential + - expression + - HISAT2 + - featureCounts + - EdgeR + - limmavoom + - DESeq2 + - transcriptomics + - mouse + - multiple + tools: + - limma_voom + - featurecounts + - hisat2 + update_time: '2020-08-08' + versions: 35 +- create_time: '2020-01-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 86838846a266181d + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=86838846a266181d + name: Copy of AptaSuite Ready 20 000 shared by user monika_cz + number_of_steps: null + source: https://usegalaxy.org + tags: + - imported + tools: + - fastq_manipulation + - sort1 + - cshl_fastx_reverse_complement + - fastq_to_fasta_python + - tp_replace_in_line + - cshl_fastx_collapser + - fasta2tab + - join1 + - Grep1 + - fastq_to_tabular + - tp_head_tool + - tp_find_and_replace + - Show beginning1 + - tab2fasta + - fastq_groomer + - tabular_to_fastq + update_time: '2020-07-21' + versions: 6 +- create_time: '2020-03-31' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + - Statistical calculation + - Phylogenetic tree generation + edam_topic: [] + id: a46ad0b9240d1a13 + latest_version: 30 + license: null + link: https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13 + name: Viral Evolution Analysis (NCBI Data) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - Cut1 + - split_file_to_collection + - hyphy_slac + - sarscov2summary + - __RELABEL_FROM_FILE__ + - kc-align + - hyphy_fel + - hyphy_meme + - hyphy_prime + - param_value_from_file + - rapidnj + - sarscov2formatter + update_time: '2020-07-10' + versions: 30 +- create_time: '2020-06-20' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: 0b1fa3e8d05d6e53 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0b1fa3e8d05d6e53 + name: 'Workflow constructed from history polymorphism ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - lofreq_call + - samtools_stats + - bowtie2 + - freebayes + update_time: '2020-06-25' + versions: 1 +- create_time: '2019-10-28' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7551458d929355c2 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=7551458d929355c2 + name: Powell et al. - Environmental Enrichment RNA-seq Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - stringtie + - multiqc + - stringtie_merge + - hisat2 + update_time: '2020-06-22' + versions: 1 +- create_time: '2016-09-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 070e476b3aa36fbe + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=070e476b3aa36fbe + name: Example + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_replace_in_line + - tp_awk_tool + update_time: '2020-06-18' + versions: 4 +- create_time: '2020-06-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 9bace540b35b1e61 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=9bace540b35b1e61 + name: RNASeq_Bacteria_Mtb + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNASeq + - Bacteria + - FastQC + - MultiQC + - Trimmomatic + - Bowtie2 + - featureCounts + - DESeq2 + tools: + - fastqc + - trimmomatic + - multiqc + - bowtie2 + - featurecounts + - deseq2 + update_time: '2020-06-17' + versions: 7 +- create_time: '2020-06-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0f43fdfe1824e9d7 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=0f43fdfe1824e9d7 + name: Sequence analysis workflow (its output is the MetaPhylAn input) (imported + from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_fastx + - fastqc + - fastq_dump + - samtools_view + - picard_DownsampleSam + - samtool_filter2 + - cshl_fastq_quality_filter + - hisat2 + update_time: '2020-06-11' + versions: 6 +- create_time: '2020-06-04' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + - Transcriptome assembly + - Sequence alignment + - Sequence annotation + edam_topic: [] + id: 454d7310d001a4d0 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=454d7310d001a4d0 + name: HISAT2- SrtringTie, 3 rep. 2 condition + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - stringtie + - stringtie_merge + - gffcompare + - hisat2 + update_time: '2020-06-05' + versions: 4 +- create_time: '2020-06-01' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 92875b13082b5568 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=92875b13082b5568 + name: Workflow constructed from history 'mNGS0528' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastp + - bowtie2 + - hisat2 + update_time: '2020-06-01' + versions: 0 +- create_time: '2020-05-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 1e53fcd07ae5d859 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=1e53fcd07ae5d859 + name: Workflow constructed from history 'Determine DNA polymorphic sites.' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2020-05-29' + versions: 0 +- create_time: '2020-05-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: cb03300161109123 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=cb03300161109123 + name: Workflow 'variant coursera project ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sam_merge2 + - charts + - snpSift_extractFields + - Remove beginning1 + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - snpEff + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2020-05-28' + versions: 0 +- create_time: '2020-05-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0a89328e6d28dd07 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0a89328e6d28dd07 + name: Workflow constructed from history 'PD_ JHUC2_Identify DNA polymorphic sites' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2020-05-12' + versions: 0 +- create_time: '2020-05-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3324b82d4efa1a68 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=3324b82d4efa1a68 + name: Download and SE+PE Illumina Covid Variation Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - __MERGE_COLLECTION__ + - collapse_dataset + update_time: '2020-05-05' + versions: 1 +- create_time: '2020-05-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Phylogenetic analysis + - Sequence analysis + - Multiple sequence alignment + edam_topic: [] + id: e1cc0886cd27b92e + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e + name: Evolution Analysis (All Other Data) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - Cut1 + - split_file_to_collection + - hyphy_slac + - sarscov2summary + - __RELABEL_FROM_FILE__ + - kc-align + - hyphy_fel + - hyphy_meme + - iqtree + - param_value_from_file + - hyphy_prime + - sarscov2formatter + update_time: '2020-05-04' + versions: 3 +- create_time: '2020-05-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f047f29486605cdd + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f047f29486605cdd + name: Assignment May + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - gops_join_1 + - join1 + - Grouping1 + - Show beginning1 + update_time: '2020-05-03' + versions: 0 +- create_time: '2020-05-02' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Read mapping + - Primer removal + - Sequencing quality control + edam_topic: [] + id: ae523fe6c9183e58 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=ae523fe6c9183e58 + name: mapping and alignment 'project'' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cutadapt + - samtools_stats + - multiqc + - bowtie2 + update_time: '2020-05-02' + versions: 2 +- create_time: '2020-03-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3cb4fd9ff755d36e + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=3cb4fd9ff755d36e + name: Parameters from file + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - tp_sorted_uniq + - column_remove_by_header + update_time: '2020-04-22' + versions: 4 +- create_time: '2020-04-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Genome indexing + - Sequence composition calculation + - Read mapping + - Generation + - Sequence file editing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7610b7797d71993a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=7610b7797d71993a + name: ' ''SNPcalling_with_bcftool''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - bcftools_filter + - samtools_sort + - samtools_rmdup + - snpEff + - bcftools_call + - bcftools_mpileup + - seqtk_sample + - bwa_mem + update_time: '2020-04-22' + versions: 1 +- create_time: '2020-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0360984110693d9f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0360984110693d9f + name: Exon with maximum repeat on Chr 22 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - tp_easyjoin_tool + update_time: '2020-04-06' + versions: 0 +- create_time: '2020-03-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d5cba8a5ba6880fd + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d5cba8a5ba6880fd + name: BRACA2 - primer design + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - gops_join_1 + - join1 + - Grouping1 + - Show beginning1 + update_time: '2020-03-29' + versions: 0 +- create_time: '2020-03-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0ab1922bc4ea12b2 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0ab1922bc4ea12b2 + name: good primers for braca1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - Show beginning1 + - Filter1 + update_time: '2020-03-29' + versions: 1 +- create_time: '2020-03-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5d87df0cce36f772 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5d87df0cce36f772 + name: ' tute 01 again - workflow' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - join1 + - Grouping1 + - tp_cut_tool + - tp_head_tool + update_time: '2020-03-22' + versions: 1 +- create_time: '2020-03-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6e3ca91737d56374 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=6e3ca91737d56374 + name: ' tute 01' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - join1 + - Grouping1 + - tp_cut_tool + - tp_head_tool + update_time: '2020-03-21' + versions: 1 +- create_time: '2020-03-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Read summarisation + - RNA-Seq quantification + - Sequence composition calculation + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 413d7e5aa7378cf1 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=413d7e5aa7378cf1 + name: Bulk RNAseq Analysis - training course + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - htseq_count + - rna_star + - featurecounts + update_time: '2020-03-06' + versions: 6 +- create_time: '2020-02-24' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Statistical calculation + edam_topic: [] + id: 4cbb8181cfdf55d9 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=4cbb8181cfdf55d9 + name: 3x VCF caller from BAM + number_of_steps: null + source: https://usegalaxy.org + tags: + - VCF + - variant + tools: + - picard_FixMateInformation + - varscan_mpileup + - lofreq_call + - samtools_rmdup + - samtools_mpileup + - samtool_filter2 + - freebayes + update_time: '2020-03-02' + versions: 5 +- create_time: '2020-02-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Taxonomic classification + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: a89e1018a00b883c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a89e1018a00b883c + name: CallyChase + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - kraken + - trimmomatic + - kraken-translate + - kraken-report + update_time: '2020-02-28' + versions: 0 +- create_time: '2020-02-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 470b41d0e43bb46b + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=470b41d0e43bb46b + name: Coursera Final Project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sam_merge2 + - snpSift_extractFields + - Remove beginning1 + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - snpEff + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2020-02-26' + versions: 3 +- create_time: '2020-02-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Generation + - Sequencing quality control + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: 4458439388155d92 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=4458439388155d92 + name: 'COVID-19: read pre-processing from SRA data' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - picard_MergeSamFiles + - minimap2 + - multiqc + - samtool_filter2 + - bwa_mem + update_time: '2020-02-23' + versions: 2 +- create_time: '2020-02-12' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + - Formatting + - Phylogenetic tree generation (from molecular sequences) + edam_topic: [] + id: be54e57345ce7ca5 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5 + name: 'COVID-19: MCRA' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - picard_NormalizeFasta + - Remove beginning1 + - Cut1 + - collapse_dataset + - ncbi_acc_download + - rbc_mafft + - fasttree + - tp_sed_tool + - Convert characters1 + update_time: '2020-02-21' + versions: 8 +- create_time: '2020-02-11' + creators: [] + doi: '' + edam_operation: + - Sequence assembly visualisation + - Aggregation + - Genome assembly + edam_topic: [] + id: 5039ae2c81d0aba8 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=5039ae2c81d0aba8 + name: 'COVID-19: Assembly' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bandage_image + - spades + - unicycler + - bandage_info + update_time: '2020-02-21' + versions: 5 +- create_time: '2020-02-21' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Statistical calculation + - Sequence alignment analysis + - Local alignment + - Phylogenetic tree generation (from molecular sequences) + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: 2d1ca299c1b058f6 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6 + name: 'COVID-19: RecSel' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - hyphy_gard + - rbc_mafft + - 'EMBOSS: tranalign100' + - hyphy_absrel + - fasttree + - 'EMBOSS: transeq101' + update_time: '2020-02-21' + versions: 2 +- create_time: '2020-02-20' + creators: [] + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: 956987e628530c79 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=956987e628530c79 + name: 'COVID-19: S-gene AA' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - 'EMBOSS: tranalign100' + - 'EMBOSS: transeq101' + - rbc_mafft + update_time: '2020-02-20' + versions: 2 +- create_time: '2020-02-14' + creators: [] + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: f737593a1db217c8 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=f737593a1db217c8 + name: Coronavirus Spike Protein Alignments + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - 'EMBOSS: tranalign100' + - 'EMBOSS: transeq101' + - rbc_mafft + update_time: '2020-02-18' + versions: 6 +- create_time: '2020-02-16' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Sequence analysis + - Multiple sequence alignment + - Read mapping + - Sequence alignment + edam_topic: [] + id: 23212ae74fc2d2b5 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5 + name: 'nCoV: comparison' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - collapse_dataset + - ncbi_acc_download + - tp_replace_in_line + - rbc_mafft + - snpEff_build_gb + - __FILTER_FROM_FILE__ + - iqtree + - lastz_wrapper_2 + - Filter1 + update_time: '2020-02-16' + versions: 4 +- create_time: '2020-01-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Read mapping + - Variant calling + - Sequencing quality control + edam_topic: [] + id: 0d8eb75d28fa7df2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0d8eb75d28fa7df2 + name: Desanka Lazic_Project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - bowtie2 + - samtool_filter2 + - freebayes + update_time: '2020-01-16' + versions: 0 +- create_time: '2019-12-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cd8a0662b1ae4aee + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=cd8a0662b1ae4aee + name: Zip 2 collections into list:list collection + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - __ZIP_COLLECTION__ + - __APPLY_RULES__ + update_time: '2019-12-05' + versions: 3 +- create_time: '2018-12-19' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 69363bab20c5ca6c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=69363bab20c5ca6c + name: Mutation finding + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - gatk_variant_select + - samtools_sort + - gatk_analyze_covariates + - gatk_table_recalibration + - gatk_variant_filtration + - picard_MarkDuplicates + - gatk_unified_genotyper + - gatk_count_covariates + - bwa_mem + update_time: '2019-11-24' + versions: 2 +- create_time: '2019-11-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 49f8b32c3206f76c + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=49f8b32c3206f76c + name: Workflow for Genomic Data Science with Galaxy 'peer-reviewed project' + number_of_steps: null + source: https://usegalaxy.org + tags: + - variant + - snps + - human + tools: + - fastqc + - sam_merge2 + - sort1 + - Remove beginning1 + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - bwa + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2019-11-22' + versions: 7 +- create_time: '2019-11-18' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: 9a1b4c9747bf6ae0 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=9a1b4c9747bf6ae0 + name: Gproject11.16 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - naive_variant_caller + - bowtie2 + - varscan + update_time: '2019-11-18' + versions: 1 +- create_time: '2019-10-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: be4e3c22eef28b7c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=be4e3c22eef28b7c + name: Find Exons with highest number of Features + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2019-10-27' + versions: 2 +- create_time: '2019-10-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Sequence annotation + - RNA-Seq analysis + - Transcriptome assembly + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 9c022f4028de0bc6 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=9c022f4028de0bc6 + name: LGD_Midterm_workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - tp_sort_header_tool + - stringtie + - tp_head_tool + - gffcompare + - featurecounts + - hisat2 + update_time: '2019-10-14' + versions: 4 +- create_time: '2019-10-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 529c6c68df669c51 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=529c6c68df669c51 + name: COURSE ASSIGNMENT + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2019-10-06' + versions: 0 +- create_time: '2019-09-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: a86b1f1682bb4a62 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a86b1f1682bb4a62 + name: GDS Capstone' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - htseq_count + - hisat2 + update_time: '2019-09-28' + versions: 1 +- create_time: '2019-09-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 452a86fef6e3586a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=452a86fef6e3586a + name: Genomic Data Science Capstone + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2019-09-26' + versions: 0 +- create_time: '2018-11-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b4bb2c7d8c7b5139 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b4bb2c7d8c7b5139 + name: For class + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - cat1 + - Grep1 + - fastq_groomer + - gatk_unified_genotyper + - gatk_realigner_target_creator + update_time: '2019-09-24' + versions: 0 +- create_time: '2018-10-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5719765b1136cb05 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=5719765b1136cb05 + name: '''Interproscan: Parsing GO terms from Metagenome Assembled Genomes''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Count1 + - datamash_ops + - Grep1 + - Convert characters1 + update_time: '2019-08-28' + versions: 3 +- create_time: '2019-08-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: fb903de4aa4d5090 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=fb903de4aa4d5090 + name: CAPSTONE Project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - fastq_dump + - multiqc + - featurecounts + - deseq2 + - hisat2 + update_time: '2019-08-22' + versions: 0 +- create_time: '2019-07-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 28d1e2d715476c2c + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=28d1e2d715476c2c + name: Select last n lines + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_head_tool + update_time: '2019-08-12' + versions: 3 +- create_time: '2019-02-01' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: fe764741eb374b87 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=fe764741eb374b87 + name: DESeq2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deseq2 + update_time: '2019-08-09' + versions: 4 +- create_time: '2019-08-06' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + edam_topic: [] + id: cd431e5f912d3616 + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=cd431e5f912d3616 + name: Trial + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - collection_column_join + - trimmomatic + - __FILTER_FAILED_DATASETS__ + - cshl_fastx_barcode_splitter + - __ZIP_COLLECTION__ + - featurecounts + - hisat2 + update_time: '2019-08-07' + versions: 9 +- create_time: '2019-07-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Mapping + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + - Validation + - Peak calling + - Sequencing quality control + edam_topic: [] + id: 7643e66a9b4e9c11 + latest_version: 91 + license: null + link: https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11 + name: Workshop Narrow ChIP-Seq (2 Reps Mouse) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - deeptools_plot_fingerprint + - deeptools_bigwig_compare + - deeptools_bam_coverage + - bowtie2 + - chipseeker + - multiqc + - Extract genomic DNA 1 + - deeptools_multi_bigwig_summary + - resize_coordinate_window + - macs2_callpeak + - deeptools_plot_pca + - deeptools_plot_heatmap + - deeptools_compute_matrix + - fastq_dump + - bedtools_intersectbed + - deeptools_plot_correlation + - bed2gff1 + update_time: '2019-07-30' + versions: 91 +- create_time: '2019-06-18' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - Sequence alignment + - RNA-Seq quantification + edam_topic: [] + id: 4a50ce0e9f4d4bb8 + latest_version: 16 + license: null + link: https://usegalaxy.org/published/workflow?id=4a50ce0e9f4d4bb8 + name: RNA-Seq + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - collection_column_join + - trimmomatic + - featurecounts + - hisat2 + update_time: '2019-07-30' + versions: 16 +- create_time: '2019-07-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9b5ae15bb9aaba48 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=9b5ae15bb9aaba48 + name: ATAC-seq for 4xpaired fastq cutadapt bowtie2 MACS2 2019 07 24 + number_of_steps: null + source: https://usegalaxy.org + tags: + - ATAC + - hg19 + tools: + - fastqc + - sam_merge2 + - samtools_sort + - bamFilter + - cutadapt + - macs2_callpeak + - multiqc + - bowtie2 + - samtool_filter2 + update_time: '2019-07-26' + versions: 6 +- create_time: '2019-06-22' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 80b12b6e7ac8861f + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=80b12b6e7ac8861f + name: Viral Variant Calling + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bwa_mem + - picard_MarkDuplicates + - samtools_mpileup + - freebayes + - varscan + update_time: '2019-06-22' + versions: 6 +- create_time: '2019-06-12' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 1e1a299825f27f11 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=1e1a299825f27f11 + name: Downsample interlaced uncompressed fastqsanger reads the tedious way + number_of_steps: null + source: https://usegalaxy.org + tags: + - bigdata + - downsample + - memoryfailures + - fastq + tools: + - fastqc + - tp_replace_in_line + - random_lines1 + - tp_cut_tool + - tp_easyjoin_tool + - fastq_to_tabular + - wc_gnu + - tp_sorted_uniq + - tp_find_and_replace + - multiqc + - addValue + - tabular_to_fastq + update_time: '2019-06-12' + versions: 8 +- create_time: '2018-08-03' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: e2432c4d2b61705a + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a + name: RCC Liquid Biopsy_Arnold et al._v2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - vcfcombine + - bwa_mem + - samtools_mpileup + - fastq_groomer + - varscan + update_time: '2019-05-30' + versions: 3 +- create_time: '2019-05-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 66e90021db5c6b31 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=66e90021db5c6b31 + name: '''cut'' workflow: reassign columns (fails with uncaught API exception)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + update_time: '2019-05-22' + versions: 2 +- create_time: '2019-05-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6783f54acee9df33 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=6783f54acee9df33 + name: '''cut'' workflow: no column reassignment (starts okay)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + update_time: '2019-05-22' + versions: 5 +- create_time: '2019-01-28' + creators: [] + doi: '' + edam_operation: + - Read summarisation + - RNA-Seq quantification + edam_topic: [] + id: 667b57893268d96e + latest_version: 12 + license: null + link: https://usegalaxy.org/published/workflow?id=667b57893268d96e + name: FeatureCount + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - featurecounts + update_time: '2019-05-12' + versions: 12 +- create_time: '2019-05-09' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: fbf3116881e07749 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=fbf3116881e07749 + name: FMF + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_sort + - bwa_mem + update_time: '2019-05-10' + versions: 3 +- create_time: '2019-05-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Primer removal + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 204d0da8a023d7da + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=204d0da8a023d7da + name: ' RNASeq Isabel' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - Cut1 + - trim_galore + - tp_cut_tool + - tp_tail_tool + - fastq_dump + - limma_voom + - htseq_count + - hisat2 + update_time: '2019-05-08' + versions: 10 +- create_time: '2019-05-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Primer removal + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: b3823d276917baf0 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=b3823d276917baf0 + name: RNAseq_2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - trim_galore + - tp_cut_tool + - tp_tail_tool + - fastq_dump + - limma_voom + - htseq_count + - hisat2 + update_time: '2019-05-07' + versions: 5 +- create_time: '2015-06-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ecb279a9114140ab + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=ecb279a9114140ab + name: ChIPSeqNew + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bowtie2 + - trim_galore + - macs2_callpeak + update_time: '2019-05-03' + versions: 11 +- create_time: '2019-04-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d7ea4bdc208ae5e8 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=d7ea4bdc208ae5e8 + name: BuiTran_BMS502 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - gops_join_1 + - join1 + - Grouping1 + - Show beginning1 + update_time: '2019-04-28' + versions: 3 +- create_time: '2018-10-04' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 683a0ab042fa34c9 + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=683a0ab042fa34c9 + name: Multiple Variant Analysis Pipeline + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - varscan + - gatk_indel_realigner + - samtools_rmdup + - samtools_mpileup + - gatk_unified_genotyper + - fastq_groomer + - bowtie2 + - gatk_realigner_target_creator + - freebayes + update_time: '2019-04-25' + versions: 9 +- create_time: '2019-04-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Primer removal + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 3f8e0395007c8e9e + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e + name: RNASeq-HISAT-Limma + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_filter + - cutadapt + - limma_voom + - htseq_count + - cshl_fastq_quality_filter + - hisat2 + update_time: '2019-04-22' + versions: 3 +- create_time: '2019-04-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e6a6223ef5ef85a7 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e6a6223ef5ef85a7 + name: Workflow constructed from history 'Assessment New' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - bcftools_view + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - bcftools_plugin_counts + - samtools_idxstats + - sort1 + - tp_awk_tool + - snpEff_download + - table_annovar + - samtools_flagstat + - snpEff + - samtool_filter2 + - Filter1 + - freebayes + - bwa_mem + - Cut1 + - bedtools_sortbed + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2019-04-11' + versions: 0 +- create_time: '2019-04-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 57726b39bbfb0c54 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=57726b39bbfb0c54 + name: Bioinformatics Assessment 2019 MMencias Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - bcftools_plugin_counts + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - snpEff_download + - table_annovar + - snpEff + - samtools_flagstat + - samtool_filter2 + - Filter1 + - freebayes + - bwa_mem + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2019-04-04' + versions: 0 +- create_time: '2019-04-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 0843c6f15eae2f15 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0843c6f15eae2f15 + name: Workflow constructed from history 'NGS ASSESMENT DATA BIOINFORMATICS ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - bcftools_view + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - bcftools_plugin_counts + - samtools_idxstats + - bam_to_sam + - sort1 + - tp_awk_tool + - snpEff_download + - table_annovar + - samtools_flagstat + - snpEff + - samtool_filter2 + - Filter1 + - freebayes + - bwa_mem + - Cut1 + - bedtools_sortbed + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2019-04-04' + versions: 0 +- create_time: '2019-04-01' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Read pre-processing + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Primer removal + edam_topic: [] + id: eedbd4e9caca6195 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=eedbd4e9caca6195 + name: Virus + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bwa + - bowtie2 + - trim_galore + - bedtools_bamtofastq + update_time: '2019-04-03' + versions: 2 +- create_time: '2019-04-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4ed9f54caa932479 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4ed9f54caa932479 + name: Workflow constructed from history 'Bioinformatics Data Handling Assessment + 2019' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - bcftools_view + - vcf2tsv + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - bcftools_plugin_counts + - samtools_idxstats + - bam_to_sam + - sort1 + - tp_cut_tool + - tp_awk_tool + - snpEff_download + - table_annovar + - samtools_flagstat + - snpEff + - samtool_filter2 + - Filter1 + - freebayes + - bwa_mem + - Cut1 + - bedtools_sortbed + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2019-04-03' + versions: 0 +- create_time: '2019-01-18' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: aef91b21e3b72f70 + latest_version: 15 + license: null + link: https://usegalaxy.org/published/workflow?id=aef91b21e3b72f70 + name: Bam_to_consensus_fasta + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_masker_by_quality + - gatk_variant_filtration + - gatk_unified_genotyper + - bcftools_consensus + - bwa_mem + update_time: '2019-04-02' + versions: 15 +- create_time: '2019-03-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 049e6609da2b67c4 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=049e6609da2b67c4 + name: '''Candidate Number 8941: ngs-genmed-bioinformatics-assesment. Apr2019''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - samtools_idxstats + - bam_to_sam + - sort1 + - snpEff_databases + - snpEff_download + - table_annovar + - samtools_flagstat + - snpEff + - samtool_filter2 + - Filter1 + - freebayes + - bwa_mem + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2019-04-02' + versions: 0 +- create_time: '2018-04-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 41efc922cf146e0c + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=41efc922cf146e0c + name: fastqc-trimgalore-mapwithbwa-filter-rmdup-fastqc*correctversion* + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trim_galore + - bamFilter + - samtools_rmdup + - bwa + update_time: '2019-04-01' + versions: 7 +- create_time: '2019-03-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 958f78270fc8f55c + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=958f78270fc8f55c + name: FROM FASTQ TO CONSENSUS + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bcftools_consensus + - fastq_masker_by_quality + - trimmomatic + - trim_galore + - picard_CleanSam + - bwa + - gatk_variant_filtration + - multiqc + - picard_MarkDuplicates + - gatk_unified_genotyper + - samtool_filter2 + update_time: '2019-03-27' + versions: 11 +- create_time: '2019-03-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ebbcdc389aad0eb8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ebbcdc389aad0eb8 + name: Workflow constructed from history 'NGS Assessment' P1705901 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - bcftools_view + - picard_CollectInsertSizeMetrics + - Summary_Statistics1 + - vcffilter2 + - bcftools_plugin_counts + - samtools_idxstats + - bam_to_sam + - sort1 + - tp_awk_tool + - snpEff_download + - table_annovar + - samtools_flagstat + - snpEff + - samtool_filter2 + - Filter1 + - freebayes + - bwa_mem + - Cut1 + - bedtools_sortbed + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2019-03-26' + versions: 0 +- create_time: '2018-05-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - RNA-Seq quantification + - Sequence composition calculation + - Read pre-processing + - Read summarisation + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 48adcc44fe62a99c + latest_version: 19 + license: null + link: https://usegalaxy.org/published/workflow?id=48adcc44fe62a99c + name: microRNA Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_filter + - bowtie_wrapper + - trim_galore + - fastq_groomer + - featurecounts + update_time: '2019-03-25' + versions: 19 +- create_time: '2019-03-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Read mapping + - Variant calling + - Sequencing quality control + edam_topic: [] + id: 528ed34505b1a993 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=528ed34505b1a993 + name: Workflow constructed from history 'CHEN LI CHENG Course Project' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - bowtie2 + - freebayes + update_time: '2019-03-22' + versions: 0 +- create_time: '2019-03-20' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Visualisation + - Taxonomic classification + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 23968e34d424d78e + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=23968e34d424d78e + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - mothur_otu_association + update_time: '2019-03-21' + versions: 4 +- create_time: '2019-03-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 85f576c991c3d6f1 + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=85f576c991c3d6f1 + name: create trinity.fasta.gene_trans_map + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_replace_in_line + - Grep1 + update_time: '2019-03-08' + versions: 11 +- create_time: '2019-03-07' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 775e67dc75f741b8 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=775e67dc75f741b8 + name: WGS_GATK4 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - picard_MarkDuplicates + - trimmomatic + - bwa_mem + update_time: '2019-03-08' + versions: 3 +- create_time: '2019-03-05' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 68d41ffbf92b2a8e + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=68d41ffbf92b2a8e + name: subset-vcf-to-annovar-filteres-vars + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - bcftools_view + - vcf2tsv + - bedtools_sortbed + - tp_cut_tool + - tp_awk_tool + update_time: '2019-03-07' + versions: 8 +- create_time: '2019-03-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5fa548beeb1411f2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5fa548beeb1411f2 + name: Alignment_Variant_Calling_and_Filtering-v0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2019-03-05' + versions: 0 +- create_time: '2019-03-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c95fc8692a886a59 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c95fc8692a886a59 + name: 'Alignment_Variant_Calling_and_Filtering-v0.1 DT ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2019-03-04' + versions: 0 +- create_time: '2019-03-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 31acbfc6d3775846 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=31acbfc6d3775846 + name: NGS workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2019-03-04' + versions: 1 +- create_time: '2019-03-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: af5acb5dd7bfac56 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=af5acb5dd7bfac56 + name: VS_Alignment_Variant_Calling_and_Filtering-v0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2019-03-04' + versions: 0 +- create_time: '2019-01-26' + creators: [] + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 57165345b898b978 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=57165345b898b978 + name: RSeQC + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rseqc_read_duplication + update_time: '2019-03-04' + versions: 2 +- create_time: '2019-03-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 415c7152cb78e86f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=415c7152cb78e86f + name: ngs-dnaseq-bwa-freebayes-annovar-snpeff-basic-pipeline-19-03-v0.0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: + - bwa + - freebayes + - genmedmsc + - illumina + - workshop + - 2019-03 + - annovar + - snpeff + tools: + - fastqc + - trimmomatic + - vcf2tsv + - picard_CollectInsertSizeMetrics + - vcffilter2 + - bcftools_plugin_counts + - samtools_idxstats + - Count1 + - snpEff_databases + - snpEff_download + - table_annovar + - snpEff + - samtools_flagstat + - samtool_filter2 + - Filter1 + - freebayes + - bwa_mem + - bedtools_coveragebed + - picard_MarkDuplicates + update_time: '2019-03-04' + versions: 0 +- create_time: '2019-01-24' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + edam_topic: [] + id: b857482410541e1a + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=b857482410541e1a + name: Alignment with HISAT2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - hisat2 + update_time: '2019-03-04' + versions: 4 +- create_time: '2019-01-09' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d10d692b30b89cca + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=d10d692b30b89cca + name: Sadia L2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + update_time: '2019-03-03' + versions: 4 +- create_time: '2017-04-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: db8443163482a2e0 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=db8443163482a2e0 + name: polimorphic sites in trio + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - vcfselectsamples + - picard_MergeSamFiles + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - snpEff + - picard_CleanSam + - picard_MarkDuplicates + - fastq_groomer + - freebayes + - bwa_mem + update_time: '2019-02-15' + versions: 1 +- create_time: '2019-02-15' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: defd6fc845bb960c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=defd6fc845bb960c + name: Workflow constructed from history 'chI-sequence Analilysis with Macs' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - peakcalling_macs + - bowtie2 + update_time: '2019-02-15' + versions: 1 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: bb8609e8d2d4bd89 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=bb8609e8d2d4bd89 + name: 'NrD Workflow: 7 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2019-02-11' + versions: 4 +- create_time: '2019-02-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: bd587951f475533a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=bd587951f475533a + name: 'Online Activity 1 BIO ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - gops_join_1 + - CONVERTER_interval_to_bed_0 + - join1 + - Grouping1 + - tp_head_tool + update_time: '2019-02-11' + versions: 0 +- create_time: '2018-12-24' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6c49d9c25ba4ddf5 + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=6c49d9c25ba4ddf5 + name: RNAseq D.A + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - samtools_flagstat + - cshl_fastq_quality_filter + - hisat2 + update_time: '2019-02-11' + versions: 11 +- create_time: '2018-10-08' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Multiple sequence alignment + - Global alignment + edam_topic: [] + id: 8d8e8927d63803ef + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=8d8e8927d63803ef + name: Workflow for Campylobacter jejuni Lipooliogosaccharide biosynthesis locus + typing + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - collapse_dataset + - tp_cat + - rbc_mafft + - fasta2tab + - 'EMBOSS: extractseq35' + - tab2fasta + update_time: '2019-02-10' + versions: 3 +- create_time: '2019-02-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3565de0b5f5da36f + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=3565de0b5f5da36f + name: Workflow for Coursera Assignment - Latest MM + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2019-02-06' + versions: 1 +- create_time: '2019-01-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1576c383e543a2cb + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=1576c383e543a2cb + name: RmDup + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_rmdup + update_time: '2019-02-06' + versions: 1 +- create_time: '2019-01-10' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: e6b48a02789d1879 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e6b48a02789d1879 + name: NGS_Data_Practice_Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - naive_variant_caller + - bowtie2 + - samtool_filter2 + update_time: '2019-01-10' + versions: 0 +- create_time: '2018-11-30' + creators: [] + doi: '' + edam_operation: + - Gene expression profiling + edam_topic: [] + id: 7d9bf3437e0a3d27 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=7d9bf3437e0a3d27 + name: From FASTQ to TPM + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - kallisto_quant + update_time: '2019-01-03' + versions: 6 +- create_time: '2019-01-03' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Sequencing quality control + edam_topic: [] + id: 36bd1c3d32150b90 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=36bd1c3d32150b90 + name: Workflow constructed from history 'Assignment 4 History' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_SortSam + - bwa_wrapper + - picard_AddOrReplaceReadGroups + - vcffilter2 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2019-01-03' + versions: 2 +- create_time: '2018-12-21' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Data handling + - Read pre-processing + - Sequence alignment + - Primer removal + edam_topic: [] + id: 5fc0c7c65edc7457 + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=5fc0c7c65edc7457 + name: Unpaired RNA-Seq from SRA + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rna_star + - fastq_dump + - trim_galore + update_time: '2019-01-02' + versions: 11 +- create_time: '2018-12-07' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 762f23f5a621433d + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=762f23f5a621433d + name: Transfered fragments (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bam_to_sam + - Grep1 + - sam_to_bam + - samtools_flagstat + - sam_to_fastq + - bwa_mem + update_time: '2018-12-07' + versions: 0 +- create_time: '2018-12-07' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 2cfdacee3eaf0f13 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=2cfdacee3eaf0f13 + name: Mutation analysis (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk3 + - bwa_mem + update_time: '2018-12-07' + versions: 0 +- create_time: '2018-04-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 207b8de8509c572c + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=207b8de8509c572c + name: RCB314:mapping, assembly and differential expression analysis workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cufflinks + - tophat2 + - cuffmerge + - cuffdiff + update_time: '2018-12-04' + versions: 6 +- create_time: '2018-10-17' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: ba5ea0a943d4359d + latest_version: 15 + license: null + link: https://usegalaxy.org/published/workflow?id=ba5ea0a943d4359d + name: Finder of Mutation Variants + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - gatk_variant_select + - samtools_sort + - gatk_analyze_covariates + - gatk_table_recalibration + - gatk_variant_filtration + - picard_MarkDuplicates + - gatk_unified_genotyper + - gatk_count_covariates + - bwa_mem + update_time: '2018-11-30' + versions: 15 +- create_time: '2018-11-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: eba52e61bef90dd3 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=eba52e61bef90dd3 + name: Workflow Alvaro Benitez + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2018-11-13' + versions: 1 +- create_time: '2018-11-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7da0b02000e3b9e8 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=7da0b02000e3b9e8 + name: saf-to-gtf + number_of_steps: null + source: https://usegalaxy.org + tags: + - saf + - gtf + tools: + - Remove beginning1 + - Cut1 + - Add_a_column1 + - tp_replace_in_column + - Grep1 + - bed2gff1 + - addValue + update_time: '2018-11-13' + versions: 3 +- create_time: '2018-10-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: db7989d9479c80aa + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=db7989d9479c80aa + name: "Workflow pr\xE1ctica1" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - tp_head_tool + - comp1 + update_time: '2018-11-08' + versions: 2 +- create_time: '2018-11-07' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + - Nucleic acid sequence analysis + edam_topic: [] + id: 385ac7ec85e37e3e + latest_version: 17 + license: null + link: https://usegalaxy.org/published/workflow?id=385ac7ec85e37e3e + name: RNAseq1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - htseq_count + - hisat2 + update_time: '2018-11-08' + versions: 17 +- create_time: '2018-11-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a97f55f0d098b07e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a97f55f0d098b07e + name: G101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - gops_join_1 + - join1 + - Grouping1 + - Show beginning1 + update_time: '2018-11-08' + versions: 0 +- create_time: '2018-11-05' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 27327a985fa9147f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=27327a985fa9147f + name: trimm_multiqc + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - multiqc + - trimmomatic + update_time: '2018-11-05' + versions: 0 +- create_time: '2018-10-25' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Genome assembly + - Genome indexing + - Sequence composition calculation + - Sequence file editing + - Read mapping + - Aggregation + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 69514a75e4c9af08 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=69514a75e4c9af08 + name: SBNunez-Zavala + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - unicycler + - bwa + - naive_variant_caller + - seqtk_trimfq + - bwa_mem + update_time: '2018-10-25' + versions: 1 +- create_time: '2018-08-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9e487f763daa66c0 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=9e487f763daa66c0 + name: SSM Variant Subtraction + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + - vcfvcfintersect + update_time: '2018-10-16' + versions: 2 +- create_time: '2017-12-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c4a1246974f279c5 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=c4a1246974f279c5 + name: SSM Variant Detection + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - picard_ARRG + - rgPicardMarkDups + - vcfcombine + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - sam_pileup + - sam_to_bam + - gatk_realigner_target_creator + - varscan + update_time: '2018-10-16' + versions: 2 +- create_time: '2018-10-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 84aa86200ff74b4a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=84aa86200ff74b4a + name: For class + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - cat1 + - Grep1 + - fastq_groomer + - gatk_unified_genotyper + - gatk_realigner_target_creator + update_time: '2018-10-08' + versions: 0 +- create_time: '2018-09-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e4f1cce653812a22 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e4f1cce653812a22 + name: JGooch SELEX Processing + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - fastq_to_fasta_python + - cshl_fastx_collapser + - fasta2tab + - fastq_paired_end_joiner + - tp_awk_tool + - Convert characters1 + - tab2fasta + - tp_find_and_replace + - trimmer + - addValue + update_time: '2018-09-11' + versions: 1 +- create_time: '2018-09-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 62b052f47ccf0a8c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=62b052f47ccf0a8c + name: Workflow constructed from history 'My Project2' + number_of_steps: null + source: https://usegalaxy.org + tags: + - Polymorphism + tools: + - fastqc + - picard_MergeSamFiles + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2018-09-04' + versions: 0 +- create_time: '2018-08-15' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Peak calling + - Sequence composition calculation + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 4a95226c24ccbf3c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=4a95226c24ccbf3c + name: ChIP-Seq Human + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - deeptools_plot_heatmap + - samtools_sort + - deeptools_bam_compare + - deeptools_compute_matrix + - deeptools_multi_bam_summary + - deeptools_plot_fingerprint + - deeptools_plot_correlation + - macs2_callpeak + - bowtie2 + update_time: '2018-08-16' + versions: 1 +- create_time: '2018-08-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Peak calling + - Sequence composition calculation + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 57fdd0bae83f2c97 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=57fdd0bae83f2c97 + name: ChIP-seq >30 min + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - deeptools_plot_heatmap + - samtools_sort + - deeptools_bam_compare + - deeptools_compute_matrix + - deeptools_multi_bam_summary + - deeptools_plot_fingerprint + - deeptools_plot_correlation + - macs2_callpeak + - bowtie2 + update_time: '2018-08-16' + versions: 5 +- create_time: '2018-07-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Read mapping + - Primer removal + - Sequencing quality control + edam_topic: [] + id: bb9e69ae66c3d916 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=bb9e69ae66c3d916 + name: RNA-Seq (2hr mice) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_SortSam + - cufflinks + - trim_galore + - bowtie2 + update_time: '2018-08-16' + versions: 2 +- create_time: '2018-08-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Read mapping + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 0f3f91de5f022b6e + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0f3f91de5f022b6e + name: RNA-Seq Human + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cufflinks + - samtools_sort + - trim_galore + - bowtie2 + update_time: '2018-08-16' + versions: 1 +- create_time: '2015-07-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 746f4eef47648b26 + latest_version: 17 + license: null + link: https://usegalaxy.org/published/workflow?id=746f4eef47648b26 + name: 'Abundance NrD Analysis Workflow: 2 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Count1 + - Cut1 + - Add_a_column1 + - XY_Plot_1 + - Filter1 + update_time: '2018-08-15' + versions: 17 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1a6f552cfe798883 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=1a6f552cfe798883 + name: 'NrD Workflow: 11 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2018-08-14' + versions: 3 +- create_time: '2018-08-08' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: a383ce2e2bc3c7b9 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a383ce2e2bc3c7b9 + name: 16S Workflow with Mothur program + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - mothur_summary_seqs + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_unique_seqs + - mothur_align_seqs + update_time: '2018-08-08' + versions: 1 +- create_time: '2018-08-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Aggregation + - Sequencing quality control + edam_topic: [] + id: db0671862a57968d + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=db0671862a57968d + name: Workflow constructed from history '49484' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - unicycler + update_time: '2018-08-02' + versions: 0 +- create_time: '2018-08-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a036991efb5503ab + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a036991efb5503ab + name: Workflow constructed from history 'RNA-seq' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cufflinks + - tophat2 + - cuffmerge + - cuffdiff + update_time: '2018-08-01' + versions: 0 +- create_time: '2018-07-31' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + edam_topic: [] + id: 9efb061a87bc9f4d + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=9efb061a87bc9f4d + name: Unmapped reads analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cshl_fasta_nucleotides_changer + - cshl_fastx_collapser + - hisat2 + update_time: '2018-07-31' + versions: 1 +- create_time: '2018-07-21' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: cbfdd5c8261fea57 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=cbfdd5c8261fea57 + name: Du Novo GTN tutorial - Variant calling + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - allele_counts_1 + - bwa_mem + - naive_variant_caller + - bamleftalign + - Filter1 + update_time: '2018-07-24' + versions: 6 +- create_time: '2018-07-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 77e8d68500c14660 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=77e8d68500c14660 + name: Du Novo GTN tutorial - Make consensus sequences + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sequence_content_trimmer + - correct_barcodes + - make_families + - dunovo + - align_families + update_time: '2018-07-22' + versions: 5 +- create_time: '2018-06-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 10d8d47f97afc999 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=10d8d47f97afc999 + name: Workflow constructed from history 'Alignment_Variant_Calling_and_Filtering-v0.1' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-06-29' + versions: 0 +- create_time: '2018-06-23' + creators: [] + doi: '' + edam_operation: + - Formatting + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Read mapping + - Variant calling + - Generation + - Sequence alignment + edam_topic: [] + id: 38cc6577c9b15275 + latest_version: 34 + license: null + link: https://usegalaxy.org/published/workflow?id=38cc6577c9b15275 + name: Coursera_DatasciencewithGalaxy_Programmingassignment + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - picard_MergeSamFiles + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2018-06-25' + versions: 34 +- create_time: '2018-05-30' + creators: [] + doi: '' + edam_operation: + - Mapping + - Read mapping + - Data handling + edam_topic: [] + id: 73f5b1a6fd3c703f + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=73f5b1a6fd3c703f + name: Map-RSeQC + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_sort + - bedtools_sortbed + - Grep1 + - tp_sorted_uniq + - gff2bed1 + - rseqc_RPKM_saturation + - bowtie2 + update_time: '2018-06-06' + versions: 4 +- create_time: '2018-05-17' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 64fa13bb48fcd7df + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=64fa13bb48fcd7df + name: Mothur turorial + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_chimera_uchime + - mothur_remove_seqs + - mothur_get_groups + - mothur_seq_error + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_unique_seqs + - mothur_align_seqs + - mothur_classify_seqs + - mothur_remove_lineage + - mothur_pre_cluster + update_time: '2018-05-17' + versions: 1 +- create_time: '2018-05-09' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + edam_topic: [] + id: 10fa713ca3076a47 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=10fa713ca3076a47 + name: Workflow constructed from history 'RNA-Seq_aula3' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rna_star + - cuffmerge + - cuffdiff + - cufflinks + update_time: '2018-05-09' + versions: 0 +- create_time: '2018-05-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 67e56a9919ed84f7 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=67e56a9919ed84f7 + name: Workflow constructed from history 'Beeta_M_Polymorphic_sites' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - vcfselectsamples + - picard_MergeSamFiles + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - cat1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2018-05-08' + versions: 0 +- create_time: '2018-05-01' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Primer removal + - Sequence trimming + - Generation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2219c4aa7eb8cfb8 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=2219c4aa7eb8cfb8 + name: Workflow on read mapping with BWA + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - tp_sort_header_tool + - trim_galore + - bamFilter + - bwa + - samtools_flagstat + - deeptools_bam_coverage + update_time: '2018-05-07' + versions: 5 +- create_time: '2018-03-05' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + edam_topic: [] + id: 2ec3e326c51d3147 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147 + name: Workflow constructed from history 'Pathogen Discovery with Kraken' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - kraken + - kraken-translate + - tp_sort_header_tool + update_time: '2018-04-10' + versions: 4 +- create_time: '2018-04-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 39c054f4a3e42a25 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=39c054f4a3e42a25 + name: Workflow constructed from history 'Assignment run workflow' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2018-04-09' + versions: 0 +- create_time: '2018-04-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 86be1351ffb6498c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=86be1351ffb6498c + name: Workflow 'RNA-seq_Course_Project_NG' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2018-04-09' + versions: 0 +- create_time: '2018-04-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c57c820557ae9b55 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c57c820557ae9b55 + name: ' ''Bioinformatics_Assignment_workflow_MSCGM07Y_VCApril18''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-04-08' + versions: 0 +- create_time: '2018-04-08' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 3771c5db96f8f246 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=3771c5db96f8f246 + name: Galaxy RNA-seq analysis (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cuffcompare + - cufflinks + - cuffdiff + - bam_to_sam + - samtools_mpileup + - tophat2 + - cuffmerge + - fastq_groomer + - varscan + update_time: '2018-04-08' + versions: 0 +- create_time: '2018-02-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: cfd37af9d6e4cbdb + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=cfd37af9d6e4cbdb + name: Alignment_Variant_Calling_and_Filtering-v0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-04-04' + versions: 0 +- create_time: '2018-04-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d50b2df115706adb + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=d50b2df115706adb + name: Workflow constructed from history 'P1507062 assignment workflow final' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - tp_sort_header_tool + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-04-04' + versions: 1 +- create_time: '2018-04-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5cad854edbbd3b69 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5cad854edbbd3b69 + name: 'Workflow constructed from history ''imported: ngs-wes-illumina-basic-genmed-2018.01''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - snpSift_filter + - samtools_idxstats + - tp_sort_header_tool + - vcf2tsv + - Grouping1 + - picard_CollectInsertSizeMetrics + - snpEff + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-04-03' + versions: 0 +- create_time: '2018-03-31' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 4d251ecda59c87c5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4d251ecda59c87c5 + name: Bioinformatics_Assignment_Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-03-31' + versions: 0 +- create_time: '2018-03-20' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f47f0b25c1405128 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=f47f0b25c1405128 + name: 4 Replicates HISAT2/CUFFLINKS DE + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cuffcompare + - trimmomatic + - cufflinks + - cuffdiff + - cuffmerge + - fastq_groomer + - hisat2 + update_time: '2018-03-29' + versions: 4 +- create_time: '2018-03-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9d626a89800a96ca + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=9d626a89800a96ca + name: ngs-wes-illumina-hg19-bwa-freebayes-snpsift-annovar-2018.01 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - snpSift_filter + - samtools_idxstats + - tp_sort_header_tool + - picard_CollectInsertSizeMetrics + - snpEff + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-03-28' + versions: 1 +- create_time: '2018-03-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e57d595b0cde1614 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=e57d595b0cde1614 + name: ngs-hg19-bwa-freebayes-snpsift-annovar-filter-genmed-2018 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - snpSift_filter + - samtools_idxstats + - tp_sort_header_tool + - picard_CollectInsertSizeMetrics + - snpEff + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-03-26' + versions: 6 +- create_time: '2018-03-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6822f413a3b09cb4 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=6822f413a3b09cb4 + name: first workshop + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-03-03' + versions: 1 +- create_time: '2018-03-02' + creators: [] + doi: '' + edam_operation: + - Data handling + - Sequence annotation + edam_topic: [] + id: c8653e558a68eb68 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c8653e558a68eb68 + name: Utpal RNA_Seq Workflow (cds & exon calling only) from paired end Illumina + data + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gffread + - cufflinks + - samtools_sort + - fastq_dump + - tophat2 + update_time: '2018-03-02' + versions: 1 +- create_time: '2017-05-04' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 4fcfea3a6691e18b + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=4fcfea3a6691e18b + name: 01-ngs-bwa-mem-markdupe-filter + number_of_steps: null + source: https://usegalaxy.org + tags: + - bwa-mem + - cleansam + - fixmate + - hg19 + - markduplicate + - filtersam + tools: + - picard_FixMateInformation + - picard_ValidateSamFile + - picard_CleanSam + - picard_MarkDuplicates + - samtool_filter2 + - bwa_mem + update_time: '2018-03-01' + versions: 4 +- create_time: '2018-02-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: adf531bc12766c9b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=adf531bc12766c9b + name: 2Tadiso2_Alignment_Variant_Calling_and_Filtering-v0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-02-27' + versions: 0 +- create_time: '2018-02-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: dbcf0fbf5329b3fb + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=dbcf0fbf5329b3fb + name: Alignment_Variant_Calling_and_Filtering-v0.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-02-26' + versions: 0 +- create_time: '2018-02-25' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 4d04cc04954f069b + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=4d04cc04954f069b + name: In Silico + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bed_to_bigBed + - bedtools_sortbed + - bedtools_intersectbed + update_time: '2018-02-25' + versions: 4 +- create_time: '2018-02-19' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 50fb074833eb9836 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=50fb074833eb9836 + name: Workflow constructed from history 'inudoshi_desu' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + update_time: '2018-02-23' + versions: 1 +- create_time: '2018-02-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e6550f5289099efc + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e6550f5289099efc + name: Workflow constructed from history 'SN_SP' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - CONVERTER_gff_to_bed_0 + - Summary_Statistics1 + - Filter1 + - gops_coverage_1 + update_time: '2018-02-20' + versions: 0 +- create_time: '2018-02-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: df6b9760e071b91b + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=df6b9760e071b91b + name: Varient detection pipeline final + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - samtools_rmdup + - bwa + - picard_MarkDuplicates + - fastq_groomer + - bowtie2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2018-02-20' + versions: 6 +- create_time: '2018-02-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 35ec8aeeaa59f6ae + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=35ec8aeeaa59f6ae + name: Exons with the Highest number of SNPs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2018-02-19' + versions: 1 +- create_time: '2018-02-16' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Formatting + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 803215ef8142c069 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=803215ef8142c069 + name: 'Workflow ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - vcffilter2 + - picard_MarkDuplicates + - bowtie2 + - freebayes + update_time: '2018-02-16' + versions: 1 +- create_time: '2018-02-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d8d005a019fe76f7 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=d8d005a019fe76f7 + name: RNA-seq analysis from SRA PE data (hg38, genecode.v24) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - genomespace_importer + - trim_galore + - fastq_dump + - rna_star + - multiqc + - featurecounts + update_time: '2018-02-06' + versions: 2 +- create_time: '2018-01-25' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: dddd23119443b85e + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=dddd23119443b85e + name: Canonical pipeline Matthew Crabtree + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - vcffilter2 + - table_annovar + - bowtie2 + - freebayes + update_time: '2018-02-02' + versions: 10 +- create_time: '2017-11-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d3811603bbd4a940 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d3811603bbd4a940 + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - join1 + - Cut1 + update_time: '2017-12-17' + versions: 0 +- create_time: '2017-07-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0ac68ec25f3534da + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=0ac68ec25f3534da + name: edwin3.0 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cufflinks + - Extract genomic DNA 1 + - Grouping1 + - Convert characters1 + - comp1 + - Filter1 + update_time: '2017-12-11' + versions: 11 +- create_time: '2016-09-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1efb485f123233eb + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=1efb485f123233eb + name: Test Fasta - Fastq V3 + number_of_steps: null + source: https://usegalaxy.org + tags: + - Fasta + - Tabular + - FASTQ + tools: + - fasta2tab + - tabular_to_fastq + update_time: '2017-12-03' + versions: 2 +- create_time: '2017-03-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Peak calling + - Sequence composition calculation + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 21b416bcf0b8c8cf + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=21b416bcf0b8c8cf + name: Fastq to MACS, no shift model + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - macs2_callpeak + - samtools_flagstat + - fastq_groomer + - bowtie2 + update_time: '2017-12-01' + versions: 3 +- create_time: '2017-12-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e67ce2ce587a6f39 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e67ce2ce587a6f39 + name: Workflow constructed from history 'galaxy-20171201' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-12-01' + versions: 1 +- create_time: '2017-11-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c978366ac25fed40 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c978366ac25fed40 + name: Workflow 1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - tp_head_tool + - comp1 + update_time: '2017-11-30' + versions: 1 +- create_time: '2017-11-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e586940a7c93ef73 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e586940a7c93ef73 + name: work flow for BIF101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - gops_join_1 + - join1 + - Grouping1 + - Show beginning1 + update_time: '2017-11-15' + versions: 0 +- create_time: '2017-11-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cf21a13f09fcc070 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=cf21a13f09fcc070 + name: Find Exons with highest number of SNPs 'Galaxy 101 Pooja' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-11-09' + versions: 3 +- create_time: '2017-11-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 25897c7a15f29c32 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=25897c7a15f29c32 + name: "Workflow 'Microsat\xE9lites en intrones del ChrY' \xC1lvaro S\xE1nchez Villalba" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - join1 + - Grouping1 + - Show beginning1 + update_time: '2017-11-09' + versions: 0 +- create_time: '2017-11-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 889aa91c6d3f5654 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=889aa91c6d3f5654 + name: "Workflow constructed from history 'Ejercicio: An\xE1lisis en genoma completo\ + \ mediante Galaxy - MB'" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-11-09' + versions: 3 +- create_time: '2017-11-09' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 3fbaa9ae67362495 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=3fbaa9ae67362495 + name: Workflow constructed from history 'Practicals' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - tophat2 + - fastq_quality_trimmer + update_time: '2017-11-09' + versions: 1 +- create_time: '2017-11-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: eca0449a7460480c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=eca0449a7460480c + name: WF chr16-CpG en Genes + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-11-09' + versions: 1 +- create_time: '2017-10-29' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Sequence alignment + edam_topic: [] + id: 2d44e2b020bf94f8 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2d44e2b020bf94f8 + name: GenomicsDataScienceCoursera + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - vcfcombine + - Grouping1 + - table_annovar + - hisat2 + - vcffilter2 + - Filter1 + - freebayes + update_time: '2017-10-29' + versions: 1 +- create_time: '2017-10-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 68d05aae72fcd2c9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=68d05aae72fcd2c9 + name: Workflow constructed from history 'Identify DNA polymorphic sites' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2017-10-13' + versions: 0 +- create_time: '2017-06-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ff137b61d4ef1b86 + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86 + name: "Capture cibl\xE9e" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - varscan + - bam_to_sam + - vcftools_annotate + - samtools_mpileup + - bwa + - samtools_stats + - picard_CollectInsertSizeMetrics + - table_annovar + - samtools_flagstat + - picard_MarkDuplicates + - fastq_groomer + - freebayes + update_time: '2017-10-06' + versions: 10 +- create_time: '2017-09-28' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: 2d50de9b95ad0808 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=2d50de9b95ad0808 + name: differential_gene_expression + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - deseq2 + update_time: '2017-09-28' + versions: 0 +- create_time: '2017-09-26' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: 36a92f1f6d2212a4 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=36a92f1f6d2212a4 + name: RNASeqSect2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - collection_column_join + - Cut1 + - tp_easyjoin_tool + - deseq2 + - Filter1 + update_time: '2017-09-27' + versions: 3 +- create_time: '2017-09-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ccb66f80518daba3 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=ccb66f80518daba3 + name: PreprocessGF + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_find_and_replace + - Cut1 + update_time: '2017-09-27' + versions: 5 +- create_time: '2017-09-26' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - Sequence composition calculation + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: d8afd017905d6702 + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=d8afd017905d6702 + name: RNASeq + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - collection_column_join + - cshl_fastx_clipper + - Cut1 + - tp_easyjoin_tool + - htseq_count + - cshl_fastq_quality_filter + - Filter1 + - deseq2 + - hisat2 + update_time: '2017-09-27' + versions: 9 +- create_time: '2017-09-12' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - Sequence composition calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a8ddab36010ed4c3 + latest_version: 15 + license: null + link: https://usegalaxy.org/published/workflow?id=a8ddab36010ed4c3 + name: Collin Rna-seq for two groups + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - rna_star + - fastq_groomer + - deseq2 + update_time: '2017-09-18' + versions: 15 +- create_time: '2017-09-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 47e190ec408a71b1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=47e190ec408a71b1 + name: G101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - gops_join_1 + - join1 + - Grouping1 + - Show beginning1 + update_time: '2017-09-14' + versions: 0 +- create_time: '2017-09-08' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: d3eae9943ce2a62b + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=d3eae9943ce2a62b + name: jinling-coursera-project-workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - Convert characters1 + - snpEff_download + - snpEff + - vcffilter2 + - fastq_groomer + - bowtie2 + - freebayes + update_time: '2017-09-08' + versions: 1 +- create_time: '2017-09-07' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: 78db135e2aa5789d + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=78db135e2aa5789d + name: coursera-workflow-jinling + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - snpEff_download + - snpEff + - vcffilter2 + - fastq_groomer + - bowtie2 + - freebayes + update_time: '2017-09-08' + versions: 1 +- create_time: '2017-09-04' + creators: [] + doi: '' + edam_operation: + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Enrichment analysis + - Primer removal + - Differential gene expression analysis + - Sequence trimming + - Exonic splicing enhancer prediction + - Read summarisation + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + edam_topic: [] + id: 82681bd5f059e39a + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=82681bd5f059e39a + name: RNA-Seq + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffcompare + - dexseq_count + - cummerbund_to_cuffdiff + - cufflinks + - dexseq + - trim_galore + - cuffdiff + - salmon + - cummeRbund + - cuffmerge + - rna_star + - featurecounts + - deseq2 + update_time: '2017-09-04' + versions: 11 +- create_time: '2017-09-01' + creators: [] + doi: '' + edam_operation: + - Peak calling + - Enrichment analysis + - Gene regulatory network analysis + edam_topic: [] + id: 671ca26597d27579 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=671ca26597d27579 + name: 'Galaksio use case: Mouse ChIP-seq workflow' + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP-seq + tools: + - deeptools_plot_fingerprint + - deeptools_multi_bam_summary + - deeptools_plot_correlation + - macs2_callpeak + update_time: '2017-09-01' + versions: 2 +- create_time: '2017-09-01' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: f946f1309fe31ecf + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=f946f1309fe31ecf + name: 'Galaksio use case: Mouse ChIP-seq subworkflow' + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP-seq + - subworkflow + tools: + - bwa + - deeptools_bam_coverage + - samtool_filter2 + update_time: '2017-09-01' + versions: 1 +- create_time: '2017-04-11' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequence merging + - Sequencing quality control + edam_topic: [] + id: 9a1fb6ecff886358 + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358 + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - iuc_pear + - cshl_fastq_quality_filter + - cshl_fastx_artifacts_filter + - fastq_groomer + - fastq_trimmer + - cshl_fastq_to_fasta + update_time: '2017-09-01' + versions: 13 +- create_time: '2017-08-29' + creators: [] + doi: '' + edam_operation: + - Peak calling + - Enrichment analysis + - Gene regulatory network analysis + edam_topic: [] + id: a3945ef04698a1c5 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=a3945ef04698a1c5 + name: Parent Workflow ChIPSeq + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIPseq + - tutorial + tools: + - deeptools_multi_bam_summary + - deeptools_plot_fingerprint + - deeptools_plot_correlation + - macs2_callpeak + - macs2_predictd + update_time: '2017-08-29' + versions: 3 +- create_time: '2017-08-29' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 9755ee798b9c119b + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=9755ee798b9c119b + name: ChipSeq_tutorial_child1 + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIPseq + - Tutorial + tools: + - bwa + - deeptools_bam_coverage + - samtool_filter2 + update_time: '2017-08-29' + versions: 4 +- create_time: '2017-08-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9864961cc6132562 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=9864961cc6132562 + name: Intensity-per-nucleus_IFs-quantification (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - Convert characters1 + - Remove beginning1 + - mergeCols1 + update_time: '2017-08-24' + versions: 0 +- create_time: '2017-08-14' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 199d1df1df160ad1 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=199d1df1df160ad1 + name: Bam to Fasta + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bedtools_bamtobed + - bedtools_mergebed + - bedtools_getfastabed + update_time: '2017-08-14' + versions: 1 +- create_time: '2017-08-07' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Read mapping + edam_topic: [] + id: aae5b6d9beb860ba + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=aae5b6d9beb860ba + name: RNA-seq differential expression analysis + number_of_steps: null + source: https://usegalaxy.org + tags: + - Easy + tools: + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - bowtie2 + - deseq2 + update_time: '2017-08-11' + versions: 8 +- create_time: '2017-07-23' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: c24cfddfc88a97a3 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c24cfddfc88a97a3 + name: Coursera Project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - multiqc + - tp_multijoin_tool + - featurecounts + - hisat2 + update_time: '2017-07-23' + versions: 0 +- create_time: '2017-07-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 262adf3e639569e1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=262adf3e639569e1 + name: Sort BAM + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - bam_to_sam + - sam_to_bam + update_time: '2017-07-17' + versions: 0 +- create_time: '2017-07-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 46d035f814a9b4f8 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=46d035f814a9b4f8 + name: SavedAs_Galaxy project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2017-07-04' + versions: 1 +- create_time: '2017-06-30' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 4164a02a6bd70893 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=4164a02a6bd70893 + name: SavedAs_Workflow constructed from history 'Course project Galaxy-Jayabrata + Mukherjee' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sam_merge2 + - picard_AddOrReplaceReadGroups + - bwa_mem + - table_annovar + - vcffilter2 + - freebayes + update_time: '2017-06-30' + versions: 1 +- create_time: '2017-06-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: df7459b7e8acb872 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=df7459b7e8acb872 + name: Tuxedo Protocol + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - fastq_groomer + update_time: '2017-06-28' + versions: 1 +- create_time: '2017-05-23' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - RNA-Seq quantification + - Sequence alignment + - Read summarisation + - Sequence annotation + edam_topic: [] + id: 4061e061f659449b + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=4061e061f659449b + name: RNA-seq de novo transcriptome reconstruction tutorial workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - trimmomatic + - Cut1 + - stringtie + - join1 + - Convert characters1 + - gffcompare + - deeptools_bam_coverage + - Filter1 + - stringtie_merge + - featurecounts + - deseq2 + - hisat2 + update_time: '2017-06-22' + versions: 8 +- create_time: '2017-06-04' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 63e0dcf18794dbc1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=63e0dcf18794dbc1 + name: Coursera Galaxy Final Project Workflow - Rebecca Tippner-Hedges + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - vcfselectsamples + - picard_MergeSamFiles + - tp_sort_header_tool + - picard_AddOrReplaceReadGroups + - bwa_mem + - Grouping1 + - cat1 + - table_annovar + - vcffilter2 + - fastq_groomer + - freebayes + update_time: '2017-06-04' + versions: 0 +- create_time: '2017-05-31' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: fc09d17e0bce18f8 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=fc09d17e0bce18f8 + name: Workflow 'RNA Seq' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - bowtie_wrapper + - CONVERTER_bed_to_gff_0 + - fastq_dump + - featurecounts + update_time: '2017-05-31' + versions: 3 +- create_time: '2017-05-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a1047ce36ac8f871 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=a1047ce36ac8f871 + name: Callan Rules + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - tp_replace_in_line + - tp_cat + - vcf2tsv + - tp_easyjoin_tool + - cat1 + - Grep1 + - table_annovar + - Convert characters1 + - tp_sorted_uniq + - addValue + - Filter1 + update_time: '2017-05-31' + versions: 2 +- create_time: '2017-05-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8b1eedebcb94ba93 + latest_version: 18 + license: null + link: https://usegalaxy.org/published/workflow?id=8b1eedebcb94ba93 + name: MAGeCK count table to .GCT for IGV + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tp_replace_in_line + - tp_cat + - mergeCols1 + - tp_cut_tool + - tp_tail_tool + - tp_replace_in_column + - tp_head_tool + - tp_sed_tool + - wc_gnu + - Paste1 + - addValue + - datamash_transpose + update_time: '2017-05-30' + versions: 18 +- create_time: '2017-05-24' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 8b2c8c8ce121177d + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8b2c8c8ce121177d + name: Genomic Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cufflinks + - cuffquant + - cuffdiff + - bam_to_sam + - tp_cut_tool + - tophat2 + - cuffmerge + - Filter1 + update_time: '2017-05-26' + versions: 0 +- create_time: '2017-05-03' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Read mapping + - Statistical calculation + edam_topic: [] + id: c337e5265a8079d0 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=c337e5265a8079d0 + name: sara workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_paired_end_joiner + - picard_MarkDuplicates + - snpEff + - vcffilter2 + - bowtie2 + - freebayes + update_time: '2017-05-24' + versions: 3 +- create_time: '2017-05-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a4a2fa50bb0f095c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a4a2fa50bb0f095c + name: galaxy101-2017 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-05-18' + versions: 1 +- create_time: '2017-05-05' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Read mapping + - Statistical calculation + edam_topic: [] + id: 399b4543d26990f2 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=399b4543d26990f2 + name: Coursera3 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - picard_MergeSamFiles + - picard_AddOrReplaceReadGroups + - Grouping1 + - table_annovar + - vcffilter2 + - fastq_groomer + - bowtie2 + - freebayes + update_time: '2017-05-06' + versions: 1 +- create_time: '2013-03-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0769f77979798f16 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0769f77979798f16 + name: TopHat + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tophat + update_time: '2017-05-05' + versions: 1 +- create_time: '2017-05-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5a21af5ec4b0c567 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5a21af5ec4b0c567 + name: 04-ngs-filter_annovar_basic + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Filter1 + update_time: '2017-05-04' + versions: 1 +- create_time: '2017-05-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 414fa13b613b33d8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=414fa13b613b33d8 + name: Workflow constructed from history 'SNP for Trio' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - tp_sort_header_tool + - tp_cat + - bwa_mem + - Grouping1 + - table_annovar + - snpEff + - vcffilter2 + - fastq_groomer + - Show beginning1 + - freebayes + update_time: '2017-05-03' + versions: 0 +- create_time: '2017-04-09' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + edam_topic: [] + id: 2478426a119d9d93 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2478426a119d9d93 + name: Workflow constructed from history 'Course Project' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - vcfcombine + - bwa_wrapper + - vcfleftalign + - samtool_filter2 + - freebayes + update_time: '2017-04-09' + versions: 1 +- create_time: '2017-04-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 20fe561687df596c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=20fe561687df596c + name: workflow.vcf + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2017-04-08' + versions: 0 +- create_time: '2017-04-07' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 6e6651ae846d8f83 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=6e6651ae846d8f83 + name: Workflow constructed from history 'april3' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - gops_join_1 + - bwa_wrapper + - tophat2 + - comp1 + - fastq_groomer + update_time: '2017-04-07' + versions: 0 +- create_time: '2017-04-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bd184804cfddafc4 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=bd184804cfddafc4 + name: Workflow constructed from history 'Assessment1' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2017-04-03' + versions: 0 +- create_time: '2017-02-24' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9d456396b9cd79d7 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=9d456396b9cd79d7 + name: Workflow constructed from history 'POLY' (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2017-03-30' + versions: 0 +- create_time: '2017-03-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2644a8c0da3066c5 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=2644a8c0da3066c5 + name: Workflow constructed from history 'Variant_call_assignment' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2017-03-29' + versions: 0 +- create_time: '2017-03-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 61d03396ad7f25b9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=61d03396ad7f25b9 + name: Workflow constructed from history 'Alignment_variant_calling_and_filtering' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2017-03-29' + versions: 0 +- create_time: '2017-03-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f60818a405f1bbbd + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f60818a405f1bbbd + name: Assignment Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - snpEff + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2017-03-22' + versions: 0 +- create_time: '2017-03-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ef44d02a79bd28bf + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ef44d02a79bd28bf + name: Workflow constructed from history 'Bioinformatics Assignment' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - samtools_idxstats + - bam_to_sam + - vcffilter2 + - picard_CollectInsertSizeMetrics + - table_annovar + - Summary_Statistics1 + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - Filter1 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2017-03-08' + versions: 0 +- create_time: '2017-02-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: c4cde7e8d897cd25 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c4cde7e8d897cd25 + name: Exercise_3 Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trim_galore + - bwa_wrapper + - samtools_mpileup + - sam_to_bam + - fastq_groomer + update_time: '2017-02-28' + versions: 1 +- create_time: '2017-02-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e004b6e4717296cb + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e004b6e4717296cb + name: '''Galaxy 101 (2017)''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-02-27' + versions: 1 +- create_time: '2017-02-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 1d748868e78275dd + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=1d748868e78275dd + name: Polymorphism + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2017-02-11' + versions: 0 +- create_time: '2017-02-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ab50fc9309706fbc + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=ab50fc9309706fbc + name: Workflow constructed from history 'junaid asim history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-02-11' + versions: 1 +- create_time: '2017-02-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: eb77b976984afa9c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=eb77b976984afa9c + name: Galaxy101 Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - tp_head_tool + - comp1 + update_time: '2017-02-10' + versions: 2 +- create_time: '2017-02-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 77a8f79e9723d39f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=77a8f79e9723d39f + name: '''Exons vs. Repeats 2017''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - comp1 + update_time: '2017-02-10' + versions: 0 +- create_time: '2017-02-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c060cfc7463ab118 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c060cfc7463ab118 + name: Workflow constructed from history ' Galaxy 101_Assignment#2' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-02-10' + versions: 1 +- create_time: '2017-02-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d87b4e14e8e1d39e + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=d87b4e14e8e1d39e + name: Serifat"s Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2017-02-09' + versions: 1 +- create_time: '2017-01-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a824952a04335e5b + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a824952a04335e5b + name: old snpEff + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + update_time: '2017-01-18' + versions: 1 +- create_time: '2017-01-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3a4940e05e8420da + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=3a4940e05e8420da + name: old snpEff + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + - check_snpeff_candidates + - snpSift_filter + - gatk_variant_select + update_time: '2017-01-16' + versions: 2 +- create_time: '2011-04-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1d923ce15c17b1fe + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe + name: Sureselect Pack Multi-Fasta for Earray Import + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - cshl_fasta_formatter + - Cut1 + - fasta2tab + - mergeCols1 + - tab2fasta + - fasta_concatenate0 + - addValue + - fasta_compute_length + update_time: '2017-01-12' + versions: 9 +- create_time: '2017-01-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b72edafe11293d93 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=b72edafe11293d93 + name: making a VCF file + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - fastq_stats + - picard_ARRG + - rgPicardMarkDups + - snpSift_filter + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - sam_to_bam + - snpEff + - fastq_groomer + - gatk_unified_genotyper + - gatk_realigner_target_creator + - qual_stats_boxplot + - Filter1 + update_time: '2017-01-12' + versions: 2 +- create_time: '2017-01-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e3e646407e3f921d + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=e3e646407e3f921d + name: Gaps_FINAL + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - Cut1 + - tp_cat + - mergeCols1 + - Convert characters1 + - Paste1 + - addValue + - comp1 + - Show beginning1 + update_time: '2017-01-11' + versions: 11 +- create_time: '2017-01-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 165c8a58baffe64c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=165c8a58baffe64c + name: june-HA + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpSift_filter + - rgPicardMarkDups + - fastq_groomer + - gatk_unified_genotyper + - gatk_variant_select + - gatk_indel_realigner + - sam_bw_filter + - gatk_realigner_target_creator + - gatk_depth_of_coverage + - snpEff + - snp_mapping_using_wgs + - qual_stats_boxplot + - Filter1 + - fastq_stats + - picard_ARRG + - bwa_wrapper + - bedtools_genomecoveragebed_bedgraph + - check_snpeff_candidates + - sam_to_bam + update_time: '2017-01-10' + versions: 2 +- create_time: '2016-06-30' + creators: [] + doi: '' + edam_operation: + - Formatting + - Read mapping + edam_topic: [] + id: 05ed292f512db24e + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=05ed292f512db24e + name: SNP calling on single end data + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_indel_realigner + - picard_AddOrReplaceReadGroups + - samtools_rmdup + - gatk_realigner_target_creator + - bowtie2 + - gatk_unified_genotyper + update_time: '2017-01-09' + versions: 2 +- create_time: '2016-10-25' + creators: [] + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Global alignment + - Sequence analysis + - Sequence alignment + edam_topic: [] + id: 6b4ad51307a28c7f + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=6b4ad51307a28c7f + name: "PRIMER EXAMEN BIOINFORM\xC1TICA" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - 'EMBOSS: cusp17' + - 'EMBOSS: cpgreport16' + - 'EMBOSS: newcpgseek58' + - 'EMBOSS: infoseq46' + - 'EMBOSS: freak36' + - 'EMBOSS: compseq14' + update_time: '2016-12-26' + versions: 1 +- create_time: '2016-12-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4445c84aa4795a05 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=4445c84aa4795a05 + name: Creating a bed file of signficantly different genes + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - tp_cut_tool + - tp_replace_in_column + - tp_awk_tool + - Convert characters1 + - Filter1 + update_time: '2016-12-08' + versions: 7 +- create_time: '2016-11-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c4ff30a7e517e953 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c4ff30a7e517e953 + name: Chip-Seq workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2016-11-18' + versions: 0 +- create_time: '2016-11-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 11ba260b93522c22 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=11ba260b93522c22 + name: RNAseq_11092016 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - tophat2 + - samtools_stats + - trim_galore + update_time: '2016-11-16' + versions: 6 +- create_time: '2016-11-12' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Sequencing quality control + edam_topic: [] + id: 0cbab8b7044d24f9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0cbab8b7044d24f9 + name: Workflow constructed from history 'Variant Calling' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_SortSam + - bwa_wrapper + - picard_AddOrReplaceReadGroups + - vcffilter2 + - snpEff + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2016-11-12' + versions: 0 +- create_time: '2016-11-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bd00c8a7a3b7e5be + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=bd00c8a7a3b7e5be + name: '''Assignment 12/11/2016''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_SortSam + - vcffilter2 + - snpEff + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2016-11-11' + versions: 9 +- create_time: '2016-11-10' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Sequencing quality control + edam_topic: [] + id: 840a7be198dc8ae4 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=840a7be198dc8ae4 + name: NGS Assignment / Variant Calliing - Anton Mc Donnell + number_of_steps: null + source: https://usegalaxy.org + tags: + - assignment + - NGS + - Variant + - Calling + - Anton + - Mc + - Donnell + - WEEK8 + tools: + - fastqc + - trimmomatic + - picard_SortSam + - bwa_wrapper + - picard_AddOrReplaceReadGroups + - vcffilter2 + - snpEff + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2016-11-11' + versions: 0 +- create_time: '2016-11-10' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Formatting + - Sequence composition calculation + - Mapping + - Sequencing quality control + edam_topic: [] + id: 05bf642dc7c58c40 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=05bf642dc7c58c40 + name: Read alignment and variant calling procedure + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_SortSam + - bwa_wrapper + - picard_AddOrReplaceReadGroups + - vcffilter2 + - snpEff + - bedtools_coveragebed + - samtools_flagstat + - picard_MarkDuplicates + - samtool_filter2 + - freebayes + update_time: '2016-11-10' + versions: 3 +- create_time: '2016-11-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fcc39f74d5cddf12 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=fcc39f74d5cddf12 + name: galaxy101 + number_of_steps: null + source: https://usegalaxy.org + tags: + - Exons + - SNPs + tools: + - sort1 + - gops_join_1 + - Grouping1 + - tp_head_tool + - comp1 + update_time: '2016-11-06' + versions: 1 +- create_time: '2016-10-06' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 1e6a0d6395cf6221 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=1e6a0d6395cf6221 + name: Workflow constructed from history 'Variant calling Workflow Final' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - Grouping1 + - table_annovar + - picard_CleanSam + - vcffilter2 + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2016-10-06' + versions: 1 +- create_time: '2016-09-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9304cc9410a96323 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=9304cc9410a96323 + name: qwang@research.ait.ie+convert + number_of_steps: null + source: https://usegalaxy.org + tags: + - "\uFF12\uFF11\uFF13\uFF11\uFF12" + - "\uFF46\uFF44\uFF53\uFF41\uFF44" + - "\uFF41\uFF53\uFF44\uFF41" + tools: + - fasta2tab + - tabular_to_fastq + update_time: '2016-09-22' + versions: 3 +- create_time: '2016-09-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 605f03449ebef37e + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=605f03449ebef37e + name: assemble_counts + number_of_steps: null + source: https://usegalaxy.org + tags: + - asbmr2016 + tools: + - join1 + - Cut1 + update_time: '2016-09-18' + versions: 4 +- create_time: '2016-09-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: be6abf6b2c45d15e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=be6abf6b2c45d15e + name: filter_counts_updown_combined + number_of_steps: null + source: https://usegalaxy.org + tags: + - asbmr2016 + tools: + - cat1 + - join1 + - Cut1 + update_time: '2016-09-18' + versions: 0 +- create_time: '2016-09-12' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + - Nucleic acid sequence analysis + edam_topic: [] + id: 0292971d1a87abba + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=0292971d1a87abba + name: fastq2count + number_of_steps: null + source: https://usegalaxy.org + tags: + - asbmr2016 + tools: + - htseq_count + - hisat2 + update_time: '2016-09-17' + versions: 6 +- create_time: '2016-09-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4bc7ca7ad5efaff4 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=4bc7ca7ad5efaff4 + name: deseq2gene_lists + number_of_steps: null + source: https://usegalaxy.org + tags: + - asbmr2016 + tools: + - sort1 + - Cut1 + - Filter1 + update_time: '2016-09-17' + versions: 4 +- create_time: '2016-09-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ebe6ac57f3c17dc4 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=ebe6ac57f3c17dc4 + name: Workflow constructed from history 'exon sorting' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - sort1 + update_time: '2016-09-15' + versions: 1 +- create_time: '2016-08-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Generation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3d5347f1e8ee7db2 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=3d5347f1e8ee7db2 + name: Pipe 1.2 picard + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - picard_SortSam + - varscan + - samtools_mpileup + - vcf2tsv + - picard_CollectInsertSizeMetrics + - table_annovar + - picard_MarkDuplicates + - fastq_groomer + - bwa_mem + update_time: '2016-08-26' + versions: 3 +- create_time: '2016-07-13' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: fe2c0e4694c56b6b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=fe2c0e4694c56b6b + name: Transcriptome assembly (trimmomatic-tophat-cufflink) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - tophat2 + - samtools_flagstat + update_time: '2016-08-25' + versions: 0 +- create_time: '2016-08-07' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: d43b771d93f0f609 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=d43b771d93f0f609 + name: Workflow constructed from history 'Polymorphic' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - vcfcombine + - vcffilter2 + - bowtie2 + - freebayes + update_time: '2016-08-07' + versions: 1 +- create_time: '2016-07-31' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 62ae08ab1133c22f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=62ae08ab1133c22f + name: Workflow Coursera Project Prathu + number_of_steps: null + source: https://usegalaxy.org + tags: + - Polymorphism + - Hg19 + - Courseraproject + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - fastq_groomer + - freebayes + - bwa_mem + update_time: '2016-07-31' + versions: 0 +- create_time: '2016-07-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: df1fa0b73f741a9c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=df1fa0b73f741a9c + name: Workflow constructed from history 'Genomic Data Science - Galaxy' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - fastq_groomer + - freebayes + - bwa_mem + update_time: '2016-07-29' + versions: 0 +- create_time: '2016-07-25' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + edam_topic: [] + id: 75c2cf36253194c2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=75c2cf36253194c2 + name: galaxy101-2015 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - rbc_mafft + - gops_join_1 + - Grouping1 + - tp_grep_tool + - tab2fasta + - clustalw + - comp1 + - Show beginning1 + update_time: '2016-07-27' + versions: 0 +- create_time: '2016-06-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 942db650f4ed97e1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=942db650f4ed97e1 + name: SNPs_amount_Chr22 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Count1 + - tp_sort_header_tool + - gops_join_1 + - join1 + - comp1 + update_time: '2016-07-11' + versions: 0 +- create_time: '2016-06-30' + creators: [] + doi: '' + edam_operation: + - Formatting + - Read mapping + edam_topic: [] + id: ea105a8775a56837 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ea105a8775a56837 + name: SNP calling on paired end data - v2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - picard_SortSam + - gatk_indel_realigner + - samtools_rmdup + - gatk_realigner_target_creator + - bowtie2 + - gatk_unified_genotyper + update_time: '2016-06-30' + versions: 0 +- create_time: '2016-06-28' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Nucleic acid sequence analysis + edam_topic: [] + id: dcf6f201b787d148 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=dcf6f201b787d148 + name: 'RNAseq: Reference-based by nekrut' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tophat2 + - deseq2 + - htseq_count + update_time: '2016-06-29' + versions: 4 +- create_time: '2016-06-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 5aa2caa2dcae1477 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5aa2caa2dcae1477 + name: Bacterial RNA-seq + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bowtie_wrapper + - samtools_sort + - stringtie + - cuffdiff + - cuffmerge + - sam_to_bam + - fastq_groomer + - Filter1 + update_time: '2016-06-26' + versions: 1 +- create_time: '2016-06-15' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 091896754bcc8ec1 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=091896754bcc8ec1 + name: Workflow_Biseq data preparation + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_filter + - fastq_to_fasta_python + - cshl_fastx_collapser + - fastq_groomer + update_time: '2016-06-17' + versions: 1 +- create_time: '2016-05-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Peak calling + - Sequence composition calculation + - Mapping + - Enrichment analysis + - Gene regulatory network analysis + - Sequencing quality control + edam_topic: [] + id: 07739fbbd53755f6 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=07739fbbd53755f6 + name: No input ChIP-Seq Analysis for intersect + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - histogram_rpy + - trimmomatic + - Cut1 + - bowtie_wrapper + - bedtools_bamtobed + - Add_a_column1 + - sam_bw_filter + - sam_to_bam + - macs2_callpeak + - samtools_flagstat + - wig_to_bigWig + - fastq_groomer + - Filter1 + update_time: '2016-06-13' + versions: 6 +- create_time: '2016-06-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9d2d8c39b63d8ef0 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=9d2d8c39b63d8ef0 + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - bwa_wrapper + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - bwa + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2016-06-11' + versions: 0 +- create_time: '2016-06-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 31e73cdaa0fb70c3 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=31e73cdaa0fb70c3 + name: GigaScience Example 2 -- chicken (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - gops_join_1 + - gd_sum_gd_snp + - gd_specify + - gd_find_intervals + - Filter1 + update_time: '2016-06-09' + versions: 0 +- create_time: '2016-05-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 42e44066338bdcdd + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=42e44066338bdcdd + name: GigaScience Example 1C -- aye-aye diversity (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gd_specify + - gd_nucleotide_diversity_pi + update_time: '2016-06-09' + versions: 0 +- create_time: '2016-05-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 25adc55d2a26e34b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=25adc55d2a26e34b + name: GigaScience Example 1B -- aye-aye FST (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gd_filter_gd_snp + - gd_add_fst_column + - gd_average_fst + - histogram_rpy + - gd_specify + update_time: '2016-06-09' + versions: 0 +- create_time: '2016-06-08' + creators: [] + doi: '' + edam_operation: + - Formatting + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Genome indexing + - Read mapping + - Variant calling + - Generation + - Sequence alignment + edam_topic: [] + id: 202648c6c615929b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=202648c6c615929b + name: Workflow constructed from history 'Coursera Galaxy' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - picard_MergeSamFiles + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2016-06-08' + versions: 0 +- create_time: '2016-01-21' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Generation + - Sequence alignment + edam_topic: [] + id: 5b2a0da883be03b7 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=5b2a0da883be03b7 + name: Duplex Analysis from Reads + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - picard_MergeSamFiles + - duplex + - sequence_content_trimmer + - bwa_mem + - make_families + - bwa + - naive_variant_caller + - allele_counts_1 + - Filter1 + - fastq_combiner + - align_families + update_time: '2016-06-08' + versions: 2 +- create_time: '2016-06-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d3e656ab45f40c11 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d3e656ab45f40c11 + name: Workflow constructed from history 'VCF project' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - vcfcombine + - picard_AddOrReplaceReadGroups + - bwa_mem + - table_annovar + - fastq_groomer + - freebayes + update_time: '2016-06-05' + versions: 0 +- create_time: '2016-06-04' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + - Sequence motif recognition + - Sequence cluster visualisation + - Sequence visualisation + edam_topic: [] + id: 042758b8a8c5ac80 + latest_version: 14 + license: null + link: https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80 + name: final_workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Count1 + - Remove beginning1 + - rgweblogo3 + - hgv_david + - Grouping1 + - tp_replace_in_column + - gd_new_oscar + - tp_sorted_uniq + - clustalw + - Filter1 + update_time: '2016-06-05' + versions: 14 +- create_time: '2016-06-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 9b32025036bdacb9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=9b32025036bdacb9 + name: Galaxy Project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - Filter1 + - freebayes + - bwa_mem + update_time: '2016-06-05' + versions: 0 +- create_time: '2016-06-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ad6143e2f74e1e94 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ad6143e2f74e1e94 + name: Workflow constructed from history 'Assignment_1' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - vcfselectsamples + - picard_MergeSamFiles + - tp_cat + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_MarkDuplicates + - fastq_groomer + - freebayes + - bwa_mem + update_time: '2016-06-05' + versions: 0 +- create_time: '2016-06-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: baab0758f2240225 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=baab0758f2240225 + name: Calvin galaxy coursera project 2016-06-05 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - tp_sort_header_tool + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2016-06-05' + versions: 1 +- create_time: '2016-06-04' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: df6c398b2d4f1e99 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99 + name: Workflow constructed from history 'Coursera Project' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - vcfbreakcreatemulti + - trimmomatic + - vcfselectsamples + - Grouping1 + - cat1 + - Grep1 + - table_annovar + - Filter1 + - fastq_groomer + - bowtie2 + - freebayes + update_time: '2016-06-04' + versions: 1 +- create_time: '2016-06-01' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + edam_topic: [] + id: 1bd0d7ef0aca1363 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=1bd0d7ef0aca1363 + name: RNASeq_differential_expression_analysis_2.2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - deseq2 + update_time: '2016-06-03' + versions: 3 +- create_time: '2016-05-31' + creators: [] + doi: '' + edam_operation: + - Nucleic acid sequence analysis + edam_topic: [] + id: aafa51fdc172f4c5 + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=aafa51fdc172f4c5 + name: RNASeq_differential_expression_analysis_2.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_sort + - htseq_count + update_time: '2016-06-03' + versions: 11 +- create_time: '2016-05-31' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 97064f2af2f30dc4 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=97064f2af2f30dc4 + name: RNASeq_alignment_to_a_reference + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - tophat2 + - trimmomatic + - samtools_flagstat + update_time: '2016-06-03' + versions: 1 +- create_time: '2016-05-27' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: e4e5dec116e7240b + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=e4e5dec116e7240b + name: Transcriptome assembly (trimmomatic-tophat-cufflink) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - tophat2 + - samtools_flagstat + update_time: '2016-06-03' + versions: 7 +- create_time: '2016-05-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1fd7300c8a956dd0 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=1fd7300c8a956dd0 + name: GigaScience Example 1A -- aye-aye populations + number_of_steps: null + source: https://usegalaxy.org + tags: + - aye-aye + - GigaScience + - Miller + - Galaxy + - tools + - tutorial + - to + - study + - genome + - diverstiy + - phylogenetic + - tree + - snp + - coverage + - PCA + tools: + - gd_filter_gd_snp + - gd_pca + - gd_phylogenetic_tree + - gd_population_structure + - gd_sum_gd_snp + - gd_prepare_population_structure + - gd_specify + - gd_coverage_distributions + - Filter1 + update_time: '2016-06-01' + versions: 0 +- create_time: '2016-05-30' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Read mapping + - Statistical calculation + edam_topic: [] + id: 729780617ceb80db + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=729780617ceb80db + name: '''Coursera_Assignment''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - picard_MergeSamFiles + - picard_AddOrReplaceReadGroups + - Grouping1 + - table_annovar + - vcffilter2 + - fastq_groomer + - bowtie2 + - freebayes + update_time: '2016-05-31' + versions: 0 +- create_time: '2016-05-27' + creators: [] + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a97badc83977e645 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a97badc83977e645 + name: NGS Aligments + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_dump + - Grep1 + - bwa_wrapper + - sam_to_bam + update_time: '2016-05-31' + versions: 0 +- create_time: '2016-05-05' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: b18a41e364650fee + latest_version: 34 + license: null + link: https://usegalaxy.org/published/workflow?id=b18a41e364650fee + name: trimmomatic + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - trimmomatic + - cshl_fastx_reverse_complement + - cat1 + - fastq_groomer + update_time: '2016-05-26' + versions: 34 +- create_time: '2016-05-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cd1badac800122c2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=cd1badac800122c2 + name: cassette exon 25 mai 2016_v2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - Add_a_column1 + - join1 + - mergeCols1 + - tp_cut_tool + - Convert characters1 + - tp_sorted_uniq + - addValue + - comp1 + - Filter1 + update_time: '2016-05-25' + versions: 0 +- create_time: '2016-05-24' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Formatting + - Sequencing quality control + edam_topic: [] + id: d69ea491b99016f4 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=d69ea491b99016f4 + name: 'imported: RNAseqTRAPLINE' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastx_clipper + - cufflinks + - cuffdiff + - tophat2 + - fastq_quality_trimmer + - cuffmerge + - picard_MarkDuplicates + - fastq_groomer + update_time: '2016-05-25' + versions: 3 +- create_time: '2016-05-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c17fa637bcdec86e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c17fa637bcdec86e + name: cassette exon 25 mai 2016 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - Add_a_column1 + - join1 + - mergeCols1 + - tp_cut_tool + - Convert characters1 + - tp_sorted_uniq + - addValue + - comp1 + - Filter1 + update_time: '2016-05-25' + versions: 0 +- create_time: '2016-05-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 43ca7614f6bb03d2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=43ca7614f6bb03d2 + name: Genomics Galaxy Project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2016-05-21' + versions: 0 +- create_time: '2016-04-27' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + - Sequence motif recognition + - Sequence cluster visualisation + - Sequence visualisation + edam_topic: [] + id: 18e7a954c0b6e4bc + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc + name: op + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rgweblogo3 + - clustalw + - histogram_rpy + - fasta_compute_length + - Filter1 + update_time: '2016-05-19' + versions: 13 +- create_time: '2016-05-09' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Read mapping + edam_topic: [] + id: a7ecb65025ad9c86 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=a7ecb65025ad9c86 + name: Coursera Final Project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - vcffilter2 + - bowtie2 + - freebayes + update_time: '2016-05-15' + versions: 4 +- create_time: '2015-06-24' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: a765dc267c6a5c3a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a765dc267c6a5c3a + name: neww + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_mpileup + - bowtie2 + - sam_to_bam + - varscan + update_time: '2016-05-14' + versions: 1 +- create_time: '2016-05-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 270e2cb6b02afc9c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=270e2cb6b02afc9c + name: Workflow constructed from history 'Couresera galaxy project' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - fastq_groomer + - freebayes + - bwa_mem + update_time: '2016-05-12' + versions: 0 +- create_time: '2016-05-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3108ef8b9e604c5c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=3108ef8b9e604c5c + name: Workflow relazione 4 D'Angelo Cestari + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2016-05-03' + versions: 0 +- create_time: '2016-03-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6d971192efa75c8a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=6d971192efa75c8a + name: galaxy101-2015b + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2016-05-03' + versions: 1 +- create_time: '2016-04-25' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Formatting + - Sequencing quality control + edam_topic: [] + id: 17a969fa9ac02cec + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=17a969fa9ac02cec + name: GATK Sporadic Cluster + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_ReorderSam + - picard_ARRG + - rgPicardMarkDups + - gatk_indel_realigner + - bwa_wrapper + - gatk_table_recalibration + - sam_to_bam + - vcffilter2 + - fastq_groomer + - gatk_unified_genotyper + - gatk_realigner_target_creator + - gatk_count_covariates + update_time: '2016-04-28' + versions: 0 +- create_time: '2016-04-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 865d2cc4d14ec7e1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=865d2cc4d14ec7e1 + name: Variant Call Dad Mom Kid trio MiSeq ref hg19 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - vcfcombine + - picard_SortSam + - tp_sort_header_tool + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_MarkDuplicates + - fastq_groomer + - freebayes + - bwa_mem + update_time: '2016-04-27' + versions: 0 +- create_time: '2016-04-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c8e9cb724c60144c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c8e9cb724c60144c + name: Workflow constructed from history 'mm9 unit12' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - join1 + - cat1 + - Paste1 + - Show beginning1 + - Filter1 + update_time: '2016-04-23' + versions: 1 +- create_time: '2016-04-15' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 14410527253c6f40 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=14410527253c6f40 + name: RNA-SEQ Workflow (Trimmer75bp) 150416 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sam_merge2 + - tophat2 + - fastq_groomer + - fastq_trimmer + update_time: '2016-04-21' + versions: 1 +- create_time: '2015-08-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 71e29a1ac26a94f9 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=71e29a1ac26a94f9 + name: Abundance NrD Filter Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Filter1 + update_time: '2016-04-14' + versions: 5 +- create_time: '2015-03-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b097fce5358c01e5 + latest_version: 23 + license: null + link: https://usegalaxy.org/published/workflow?id=b097fce5358c01e5 + name: Pre-Process Workflow 2 (Sel2N20 8nt barcode) + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - fasta_filter_by_length + - cshl_fastx_clipper + - cshl_fastx_collapser + - cshl_fastx_trimmer + - cshl_fastx_renamer + update_time: '2016-04-13' + versions: 23 +- create_time: '2015-03-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 87b6bac79f99c1f8 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=87b6bac79f99c1f8 + name: Pre-Process Workflow 1 + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - cshl_fastx_barcode_splitter + update_time: '2016-04-13' + versions: 6 +- create_time: '2015-07-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 86f1f231dd811b22 + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=86f1f231dd811b22 + name: Persistence NrD Filter Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Filter1 + update_time: '2016-04-12' + versions: 11 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 23bca854e549ad48 + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=23bca854e549ad48 + name: 'NrD Workflow: 10 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2016-04-12' + versions: 10 +- create_time: '2016-04-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: abc2ef77be0e5aa6 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=abc2ef77be0e5aa6 + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2016-04-09' + versions: 0 +- create_time: '2016-04-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 1d1ee1fad4e20eeb + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=1d1ee1fad4e20eeb + name: Workflow mit + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_MergeSamFiles + - bwa_wrapper + - bamFilter + - picard_AddOrReplaceReadGroups + - naive_variant_caller + - fastq_quality_trimmer + - sam_to_bam + update_time: '2016-04-07' + versions: 0 +- create_time: '2016-04-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 67559dead6cbe4a2 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=67559dead6cbe4a2 + name: se_expression + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cufflinks + - tophat2 + update_time: '2016-04-03' + versions: 1 +- create_time: '2016-03-04' + creators: [] + doi: '' + edam_operation: + - Read mapping + edam_topic: [] + id: 3680984663c813e1 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=3680984663c813e1 + name: dhfr + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_mpileup + - bowtie2 + update_time: '2016-03-29' + versions: 4 +- create_time: '2016-03-15' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 98c2e50add031fce + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=98c2e50add031fce + name: Helin Group - ChIP-seq preprocessing and reads mapping (bowtie2) + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP-seq + - bowtie + - Mapping + tools: + - fastqc + - samtools_rmdup + - fastq_quality_trimmer + - fastq_groomer + - bowtie2 + update_time: '2016-03-29' + versions: 1 +- create_time: '2016-03-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 751367180f8acb26 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=751367180f8acb26 + name: Gene expression(FPKM) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cufflinks + - tophat2 + update_time: '2016-03-21' + versions: 1 +- create_time: '2016-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c46d9db2531a44b0 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c46d9db2531a44b0 + name: Workflow constructed from history 'Exons and Repeats' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - join1 + - Cut1 + update_time: '2016-03-19' + versions: 1 +- create_time: '2016-03-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: adaa12b855e4c336 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=adaa12b855e4c336 + name: Workflow constructed from history 'rna seq' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cufflinks + - tophat2 + - cuffmerge + - cuffdiff + update_time: '2016-03-11' + versions: 0 +- create_time: '2016-03-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1e350f8ab5978571 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=1e350f8ab5978571 + name: Craig Leite Lab 10 Galaxy 101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2016-03-09' + versions: 1 +- create_time: '2016-03-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e9e8ac517480c291 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e9e8ac517480c291 + name: Aaron Szczepanek Galaxy101 lab 10 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2016-03-07' + versions: 1 +- create_time: '2016-02-17' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Formatting + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: f39603063febba82 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=f39603063febba82 + name: FreeBayes Sporadic Cluster + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_ReorderSam + - picard_ARRG + - rgPicardMarkDups + - gatk_indel_realigner + - bwa_wrapper + - gatk_table_recalibration + - sam_to_bam + - vcffilter2 + - fastq_groomer + - gatk_realigner_target_creator + - gatk_count_covariates + - freebayes + update_time: '2016-02-17' + versions: 3 +- create_time: '2016-02-17' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Formatting + - Sequencing quality control + edam_topic: [] + id: 59659e3a065c642c + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=59659e3a065c642c + name: GATK Sporadic Cluster + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - picard_ReorderSam + - picard_ARRG + - rgPicardMarkDups + - gatk_indel_realigner + - bwa_wrapper + - gatk_table_recalibration + - sam_to_bam + - vcffilter2 + - fastq_groomer + - gatk_unified_genotyper + - gatk_realigner_target_creator + - gatk_count_covariates + update_time: '2016-02-17' + versions: 6 +- create_time: '2015-07-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c50f10ecd1ac2ff9 + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=c50f10ecd1ac2ff9 + name: 'Persistence NrD Analysis Workflow: 2 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - sort1 + - Count1 + - Cut1 + - Add_a_column1 + - XY_Plot_1 + - Filter1 + update_time: '2016-02-09' + versions: 10 +- create_time: '2015-03-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2d1d69aac67a387a + latest_version: 24 + license: null + link: https://usegalaxy.org/published/workflow?id=2d1d69aac67a387a + name: 'NrD Workflow: 20 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2016-02-09' + versions: 24 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 52e099f693639115 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=52e099f693639115 + name: 'NrD Workflow: 14 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2016-02-09' + versions: 3 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5e079a9ac49a5b8c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=5e079a9ac49a5b8c + name: 'NrD Workflow: 13 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2016-02-09' + versions: 2 +- create_time: '2015-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2823322fa85c7ae1 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=2823322fa85c7ae1 + name: 'NrD Workflow: 5 rounds' + number_of_steps: null + source: https://usegalaxy.org + tags: + - aptamer + - SELEX + tools: + - Cut1 + - cshl_fastx_collapser + - fasta2tab + - join1 + - cat1 + - Convert characters1 + - Paste1 + - cshl_fastx_renamer + update_time: '2016-02-09' + versions: 4 +- create_time: '2016-01-26' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 9b81d47a468d6f99 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=9b81d47a468d6f99 + name: FASTQ to VCF + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - vcfvcfintersect + - bam_to_sam + - bwa + - picard_MarkDuplicates + - vcfbedintersect + - samtools_flagstat + - vcffilter2 + - freebayes + update_time: '2016-01-26' + versions: 8 +- create_time: '2013-11-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5c7f3d73543da895 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5c7f3d73543da895 + name: Copy of 'test' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Count1 + - fasta2tab + - fastq_to_fasta_python + update_time: '2016-01-25' + versions: 0 +- create_time: '2016-01-23' + creators: [] + doi: '' + edam_operation: + - Formatting + edam_topic: [] + id: 3686146fc097c66f + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=3686146fc097c66f + name: RNA-seq differential analysis (single-end short reads, 2 conditions, 3 replicates) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sam_merge2 + - picard_ReorderSam + - cuffdiff + - tophat + - bedtools_genomecoveragebed_bedgraph + - samtools_flagstat + - wig_to_bigWig + update_time: '2016-01-23' + versions: -1 +- create_time: '2015-02-13' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: d3a69b0b826331ef + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=d3a69b0b826331ef + name: Bed to MAF to FASTA + number_of_steps: null + source: https://usegalaxy.org + tags: + - maf + - fasta + - bed + - extract + tools: + - 'EMBOSS: revseq82' + - cat1 + - Grep1 + - Convert characters1 + - tab2fasta + - Interval2Maf1 + update_time: '2016-01-07' + versions: 1 +- create_time: '2015-12-22' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Read mapping + - Statistical calculation + edam_topic: [] + id: 53f11afc67ffb66f + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=53f11afc67ffb66f + name: '''Coursera_Assignment''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - picard_MergeSamFiles + - picard_AddOrReplaceReadGroups + - Grouping1 + - table_annovar + - vcffilter2 + - fastq_groomer + - bowtie2 + - freebayes + update_time: '2015-12-22' + versions: 0 +- create_time: '2015-07-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d77d0f5ca5cae2d1 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=d77d0f5ca5cae2d1 + name: new work + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - addValue + update_time: '2015-12-08' + versions: 2 +- create_time: '2015-11-20' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + edam_topic: [] + id: 535484d6482b80f4 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=535484d6482b80f4 + name: HW5 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_filter + - bwa_wrapper + - sam_to_bam + - samtools_flagstat + - freebayes + update_time: '2015-11-30' + versions: 7 +- create_time: '2015-11-29' + creators: [] + doi: '' + edam_operation: + - ID mapping + - Phylogenetic tree visualisation + - Database search + edam_topic: [] + id: 7294f75ad01ca7ed + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed + name: metagenomic examples + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - lca1 + - fasta2tab + - random_lines1 + - Fetch Taxonomic Ranks + - tab2fasta + - Draw_phylogram + - trim_reads + - addValue + - Filter1 + update_time: '2015-11-29' + versions: 1 +- create_time: '2015-11-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6e75ac640853d0dd + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=6e75ac640853d0dd + name: Bed -> FASTA +/- 5kB + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - join1 + - Convert characters1 + - Extract genomic DNA 1 + update_time: '2015-11-18' + versions: 10 +- create_time: '2013-06-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f201ce61becf9a80 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=f201ce61becf9a80 + name: demo to edit + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie_wrapper + - fastq_stats + - sam_to_bam + - PicardASMetrics + update_time: '2015-11-16' + versions: 1 +- create_time: '2015-11-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6d60c4491138813a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=6d60c4491138813a + name: Workflow constructed from history 'variant detection' + number_of_steps: null + source: https://usegalaxy.org + tags: + - variant + - calling + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - Grouping1 + - table_annovar + - picard_MarkDuplicates + - picard_CleanSam + - vcffilter2 + - Filter1 + - freebayes + - bwa_mem + update_time: '2015-11-12' + versions: 0 +- create_time: '2015-11-10' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + edam_topic: [] + id: 1cd08f3549cf5589 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=1cd08f3549cf5589 + name: hg19_chr17_ERR242951_vcf + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_sort + - bwa_wrapper + - fastq_quality_trimmer + - sam_to_bam + - fastq_groomer + - freebayes + update_time: '2015-11-10' + versions: 1 +- create_time: '2015-11-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5ad1bcc7e3edd504 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5ad1bcc7e3edd504 + name: Galaxy101-2015 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2015-11-06' + versions: 1 +- create_time: '2015-10-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 96b3cad73980c9d0 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=96b3cad73980c9d0 + name: galaxy101-2015 + number_of_steps: null + source: https://usegalaxy.org + tags: + - kaffashow + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2015-10-28' + versions: 2 +- create_time: '2015-10-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e7030b62a3335bd7 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e7030b62a3335bd7 + name: Workflow for Course Project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - Grouping1 + - table_annovar + - cshl_fastx_trimmer + - vcffilter2 + - freebayes + - bwa_mem + update_time: '2015-10-23' + versions: 1 +- create_time: '2015-10-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 94de815260acc3a8 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=94de815260acc3a8 + name: 50 bp SNPs Flanks Extraction + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - get_flanks1 + - Extract genomic DNA 1 + update_time: '2015-10-21' + versions: 0 +- create_time: '2015-10-13' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d89e626fa4f9434f + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f + name: Workflow constructed from history 'Sequence Quality Assessment ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastx_clipper + - fastq_quality_trimmer + - cshl_fastx_artifacts_filter + - fastq_groomer + update_time: '2015-10-13' + versions: 2 +- create_time: '2015-10-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b0c7f02cb766c819 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=b0c7f02cb766c819 + name: Workflow constructed from history 'Exons and Repeats' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - join1 + - Cut1 + update_time: '2015-10-09' + versions: 2 +- create_time: '2015-10-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 930dfd894899173e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=930dfd894899173e + name: DEG:Tuxedo2 - 2 Conditions 2 Replicates each + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffcompare + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + update_time: '2015-10-09' + versions: 0 +- create_time: '2015-10-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2ae1b71ea4634d1e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=2ae1b71ea4634d1e + name: DEG:Tuxedo2 - 2 Conditions 3 Replicates each + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffcompare + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + update_time: '2015-10-09' + versions: 0 +- create_time: '2015-10-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b4174fd0cf4f865c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b4174fd0cf4f865c + name: DEG:Tuxedo2 - 2 Conditions 1 Replicate each + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffcompare + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + update_time: '2015-10-09' + versions: 0 +- create_time: '2011-10-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6b5e56d23387e953 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=6b5e56d23387e953 + name: Cleaning fastas to remove all duplicates (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - fasta2tab + - tab2fasta + update_time: '2015-10-08' + versions: 8 +- create_time: '2015-09-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0c86c39dcd9e08c6 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0c86c39dcd9e08c6 + name: Project_CP + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2015-09-30' + versions: 0 +- create_time: '2015-09-27' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Formatting + - Read mapping + - Statistical calculation + edam_topic: [] + id: 1b4ac2bc54435ae4 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=1b4ac2bc54435ae4 + name: Project Workflow 2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - picard_AddOrReplaceReadGroups + - Grouping1 + - table_annovar + - vcffilter2 + - fastq_groomer + - bowtie2 + - freebayes + update_time: '2015-09-30' + versions: 0 +- create_time: '2015-09-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7fb3396e45c5a33b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=7fb3396e45c5a33b + name: Workflow constructed from history 'Galaxy_Course_project' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - picard_MergeSamFiles + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - table_annovar + - picard_CleanSam + - picard_MarkDuplicates + - fastq_groomer + - freebayes + - bwa_mem + update_time: '2015-09-27' + versions: 0 +- create_time: '2015-09-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 81c357e76c08ec02 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=81c357e76c08ec02 + name: Galaxy101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2015-09-26' + versions: 1 +- create_time: '2015-09-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b52561ed53c305db + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=b52561ed53c305db + name: Sep 25 2015 Indel analysis workflow (final) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - vcffilter2 + - samtools_mpileup + update_time: '2015-09-25' + versions: 4 +- create_time: '2015-09-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ca1f478276b38c4d + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ca1f478276b38c4d + name: Workflow constructed from history 'GENOMIC INTERVALS' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - join1 + - Cut1 + update_time: '2015-09-20' + versions: 0 +- create_time: '2015-08-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 96ce74b92f70d98d + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=96ce74b92f70d98d + name: "Workflow 2: An\xE1lisis de datos NGS" + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bwa_wrapper + - Grep1 + - sam_to_bam + - samtools_mpileup + - Filter1 + update_time: '2015-08-30' + versions: 3 +- create_time: '2015-04-23' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 24adb067c82862fa + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=24adb067c82862fa + name: 'Workflow 1: Tratamiento inicial de dato' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_groomer + - qual_stats_boxplot + - fastq_stats + update_time: '2015-08-30' + versions: 8 +- create_time: '2015-02-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 246da6fd63cbd49d + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=246da6fd63cbd49d + name: Workflow constructed from history 'STAT3 chip-seq 3iL hESCs E-MTAB-2042' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie_wrapper + - peakcalling_macs + - samtools_rmdup + - sam_to_bam + - samtools_flagstat + - fastq_groomer + update_time: '2015-08-15' + versions: -1 +- create_time: '2015-02-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 14f62361a15f8a24 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=14f62361a15f8a24 + name: Rearrangement Junction Detection Arabidopsis Plastid + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - fastq_filter + - comp1 + - Cut1 + - bowtie_wrapper + - Add_a_column1 + - bwa_wrapper + - fastq_to_tabular + - Paste1 + - trimmer + - fastq_groomer + - tabular_to_fastq + - Filter1 + update_time: '2015-07-30' + versions: 2 +- create_time: '2015-07-26' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 483a98be358ce21c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=483a98be358ce21c + name: Polymorphic Sites Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - bwa_mem + - Grouping1 + - table_annovar + - Convert characters1 + - vcffilter2 + - fastq_groomer + - freebayes + update_time: '2015-07-26' + versions: 0 +- create_time: '2015-07-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8bfd40faf59c9857 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=8bfd40faf59c9857 + name: Exons do crom.21 com mais SNPs + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2015-07-18' + versions: 1 +- create_time: '2015-07-01' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 3767c9c07462b777 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=3767c9c07462b777 + name: '20150701' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_filter + - cshl_fastx_clipper + - cshl_fastx_nucleotides_distribution + - cshl_fastq_quality_converter + - cshl_fastx_quality_statistics + - samtools_mpileup + - cshl_fastq_quality_boxplot + - fastq_quality_trimmer + - bamleftalign + - fastq_groomer + - bowtie2 + - bwa_mem + update_time: '2015-07-07' + versions: 1 +- create_time: '2015-05-07' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + edam_topic: [] + id: ada910fc3a68757a + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=ada910fc3a68757a + name: Keith ccRCC workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bwa_wrapper + - sam_to_bam + - table_annovar + - fastq_groomer + - fastq_trimmer + - freebayes + update_time: '2015-07-04' + versions: 6 +- create_time: '2015-06-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 45d37579deee182c + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=45d37579deee182c + name: cuffmerge_cuffdiff_exam + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffdiff + - cuffmerge + update_time: '2015-06-21' + versions: -1 +- create_time: '2015-06-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Generation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f58970e6914a1bba + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=f58970e6914a1bba + name: workflow 4 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_groomer + - samtools_stats + - bwa_mem + update_time: '2015-06-20' + versions: 1 +- create_time: '2015-06-20' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: a7ee7de93a7fb261 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a7ee7de93a7fb261 + name: ' workflow 5' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - varscan + - samtools_mpileup + - bwa_mem + update_time: '2015-06-20' + versions: 1 +- create_time: '2015-04-23' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 48dd684196c65735 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=48dd684196c65735 + name: Workflow constructed from history 'Hy5 Practicum' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cufflinks + - tophat2 + - fastq_groomer + - fastq_trimmer + update_time: '2015-06-02' + versions: 0 +- create_time: '2014-06-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f3983646b6df24bf + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=f3983646b6df24bf + name: CloudMap + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - fastq_stats + - picard_ARRG + - rgPicardMarkDups + - gatk_variant_select + - snpSift_filter + - gatk_indel_realigner + - snp_mapping_using_wgs + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - sam_to_bam + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - qual_stats_boxplot + - Filter1 + update_time: '2015-05-28' + versions: 2 +- create_time: '2014-08-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c60eca6b739a2f11 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=c60eca6b739a2f11 + name: 20140811-first-use + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2015-05-20' + versions: 1 +- create_time: '2013-06-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d2b798962b35dad9 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=d2b798962b35dad9 + name: ChIP(Helin)-2nd step + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + - Mouse + - MACS + - Illumina + tools: + - bowtie_wrapper + - peakcalling_macs + - samtools_rmdup + - sam_to_bam + - samtools_flagstat + - wig_to_bigWig + update_time: '2015-04-28' + versions: 8 +- create_time: '2015-04-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f966a8498497ee13 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=f966a8498497ee13 + name: AdvGen Lab 8 Galaxy Part 1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2015-04-21' + versions: 1 +- create_time: '2015-04-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f365c53b5024d7f1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1 + name: START_Workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - gops_intersect_1 + - cat1 + - Grep1 + - Filter1 + update_time: '2015-04-19' + versions: 0 +- create_time: '2015-04-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d7c03007ef8a618e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=d7c03007ef8a618e + name: galaxy 101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2015-04-15' + versions: 0 +- create_time: '2015-04-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f03bf569d526e51a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f03bf569d526e51a + name: ' ''Galaxy 101''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2015-04-11' + versions: 0 +- create_time: '2015-04-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b8fdf05ec7540510 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=b8fdf05ec7540510 + name: Create MEME-ChIP input FASTA file (500bp centered regions) from MACS2 summits.bed + file + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - Cut1 + - Extract genomic DNA 1 + update_time: '2015-04-10' + versions: 4 +- create_time: '2015-03-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ce2619816ce10220 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ce2619816ce10220 + name: Workflow constructed from history 'ATG7_Exom' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - rgPicFixMate + - picard_ARRG + - rgPicardMarkDups + - gatk_variant_select + - gatk_variant_combine + - gatk_indel_realigner + - gatk_analyze_covariates + - samtools_rmdup + - sam_pileup + - cat1 + - gatk_table_recalibration + - sam_to_bam + - gatk_realigner_target_creator + - gatk_unified_genotyper + - gatk_count_covariates + - Extract genomic DNA 1 + update_time: '2015-03-26' + versions: 0 +- create_time: '2015-03-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: bb9ee8e05f7042a9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9 + name: Rearrangement Junction Detection E. coli + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - fastq_filter + - comp1 + - Cut1 + - bowtie_wrapper + - Add_a_column1 + - bwa_wrapper + - fastq_to_tabular + - Paste1 + - trimmer + - fastq_groomer + - tabular_to_fastq + - Filter1 + update_time: '2015-03-23' + versions: 0 +- create_time: '2014-09-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5004f1087f5e87db + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5004f1087f5e87db + name: Rearrangement Junction Detection Human Mitochondrion + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - fastq_filter + - comp1 + - Cut1 + - bowtie_wrapper + - Add_a_column1 + - bwa_wrapper + - fastq_to_tabular + - Paste1 + - trimmer + - fastq_groomer + - tabular_to_fastq + - Filter1 + update_time: '2015-03-23' + versions: 0 +- create_time: '2014-08-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4266aa248d5b1ea4 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4 + name: Rearrangement Junction Detection Arabidopsis Mitochondrion + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - fastq_filter + - comp1 + - Cut1 + - bowtie_wrapper + - Add_a_column1 + - bwa_wrapper + - fastq_to_tabular + - Paste1 + - trimmer + - fastq_groomer + - tabular_to_fastq + - Filter1 + update_time: '2015-03-23' + versions: 2 +- create_time: '2015-02-10' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: c92c9d046b394094 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=c92c9d046b394094 + name: Fuzznuc.UCSC.Fixithere + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - 'EMBOSS: fuzznuc37' + - Convert characters1 + - gff2bed1 + - addValue + - Extract genomic DNA 1 + update_time: '2015-03-22' + versions: -1 +- create_time: '2014-12-24' + creators: [] + doi: '' + edam_operation: + - Mapping + - Read mapping + edam_topic: [] + id: c332d1bbd62e139d + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=c332d1bbd62e139d + name: Ginkgo Preprocessing + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bedtools_bamtobed + - bowtie2 + - samtool_filter2 + - samtools_rmdup + update_time: '2015-03-17' + versions: 6 +- create_time: '2013-10-22' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: a23bf4cd3bc97f2a + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=a23bf4cd3bc97f2a + name: Call_variants + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sam_merge2 + - picard_ARRG + - bwa_wrapper + - sam_bw_filter + - naive_variant_caller + - sam_to_bam + - allele_counts_1 + - Filter1 + - freebayes + update_time: '2015-03-06' + versions: 4 +- create_time: '2015-02-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ea69f4fbdbb88c71 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ea69f4fbdbb88c71 + name: Trim Reads Based on Quality (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_quality_trimmer + - fastq_filter + update_time: '2015-02-28' + versions: 0 +- create_time: '2015-02-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 56530f4d41413832 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=56530f4d41413832 + name: TF_ayalawol_302504840 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - Add_a_column1 + - gops_intersect_1 + - Grouping1 + - Summary_Statistics1 + - Show beginning1 + - Extract genomic DNA 1 + update_time: '2015-02-19' + versions: 3 +- create_time: '2015-02-03' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: b4090679dcca6ce2 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=b4090679dcca6ce2 + name: Bioinfo525_lab4 tutorial workflow + number_of_steps: null + source: https://usegalaxy.org + tags: + - rnaseq + tools: + - fastqc + - tophat2 + - cufflinks + update_time: '2015-02-09' + versions: 3 +- create_time: '2015-02-07' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 61d324b1eca6300e + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=61d324b1eca6300e + name: Lab_3_Bioinformatica + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_filter + - fastq_quality_trimmer + - fastq_groomer + - fastq_trimmer + update_time: '2015-02-07' + versions: 1 +- create_time: '2013-01-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 56d9313bc2e2720d + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=56d9313bc2e2720d + name: Picard Quality stat on BAM' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - PicardASMetrics + - PicardGCBiasMetrics + - rgEstLibComp + - PicardInsertSize + update_time: '2015-01-26' + versions: 5 +- create_time: '2012-12-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: de38adc5e22ab62f + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=de38adc5e22ab62f + name: Picard Quality stat on BAM' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - rgEstLibComp + - picard_BamIndexStats + - PicardASMetrics + - PicardGCBiasMetrics + - PicardInsertSize + update_time: '2015-01-26' + versions: 5 +- create_time: '2012-10-31' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 3c32ad1a07a66843 + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843 + name: Quality Statistics work flow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastq_quality_boxplot + - cshl_fastx_quality_statistics + - cshl_fastx_nucleotides_distribution + update_time: '2015-01-26' + versions: 9 +- create_time: '2012-10-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 38f5ab09779a6495 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=38f5ab09779a6495 + name: 'Best with HaploGATK: GATK b37 unified genotyper (old)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rgPicFixMate + - gatk_variant_annotator + - rgPicardMarkDups + - gatk_indel_realigner + - gatk_analyze_covariates + - bwa_wrapper + - sam_bw_filter + - gatk_table_recalibration + - sam_to_bam + - fastq_groomer + - gatk_unified_genotyper + - gatk_realigner_target_creator + - gatk_count_covariates + update_time: '2015-01-26' + versions: 6 +- create_time: '2012-12-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 555e68f5c807ff73 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=555e68f5c807ff73 + name: mpileup Hg19 MQ 40 BQ 30 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rgPicardMarkDups + - samtools_mpileup + - sam_bw_filter + - sam_to_bam + update_time: '2015-01-26' + versions: 6 +- create_time: '2012-12-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 99e754eaabd7f362 + latest_version: 12 + license: null + link: https://usegalaxy.org/published/workflow?id=99e754eaabd7f362 + name: Normal Cryo Mpileup with GATK and without GATK. + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rgPicFixMate + - picard_ARRG + - rgPicardMarkDups + - gatk_indel_realigner + - gatk_analyze_covariates + - bwa_wrapper + - sam_bw_filter + - samtools_mpileup + - gatk_table_recalibration + - sam_to_bam + - fastq_groomer + - gatk_realigner_target_creator + - gatk_count_covariates + update_time: '2015-01-26' + versions: 12 +- create_time: '2013-01-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 64a0203923bae319 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=64a0203923bae319 + name: Mpileup BED test + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_mpileup + update_time: '2015-01-26' + versions: 1 +- create_time: '2012-10-23' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: b7e20495b47d5b97 + latest_version: 21 + license: null + link: https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97 + name: Hg19 BWA alignment for all 4 samples with FASTQ Stat + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastx_nucleotides_distribution + - cshl_fastx_quality_statistics + - bwa_wrapper + - cshl_fastq_quality_boxplot + - fastq_groomer + update_time: '2015-01-26' + versions: 21 +- create_time: '2012-12-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 121f37a5c0562f8c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=121f37a5c0562f8c + name: Hg19 BWA alignment for all 4 samples + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_groomer + - bwa_wrapper + update_time: '2015-01-26' + versions: 2 +- create_time: '2012-12-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ca5ca2f38c1719e1 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=ca5ca2f38c1719e1 + name: Tumor FFPE aligned BAM file with GATK and without GATK + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rgPicFixMate + - picard_ARRG + - rgPicardMarkDups + - gatk_indel_realigner + - gatk_analyze_covariates + - sam_bw_filter + - gatk_table_recalibration + - sam_to_bam + - gatk_realigner_target_creator + - gatk_count_covariates + update_time: '2015-01-26' + versions: 1 +- create_time: '2015-01-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 13a550ed56b56502 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=13a550ed56b56502 + name: Workflow constructe gnene lens + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pca1 + - histogram_rpy + update_time: '2015-01-20' + versions: 1 +- create_time: '2015-01-14' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: b0a12221ce09c001 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=b0a12221ce09c001 + name: Riboseq processing workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastx_clipper + - bowtie_wrapper + update_time: '2015-01-15' + versions: 1 +- create_time: '2014-10-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3d1f4bd67ce30f99 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=3d1f4bd67ce30f99 + name: Standard strict virus mapping + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie_wrapper + - samtool_filter2 + - Grouping1 + update_time: '2014-12-09' + versions: 5 +- create_time: '2014-12-04' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: e6838c861b6beaed + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=e6838c861b6beaed + name: pre-processing_final project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_groomer + - cshl_fastx_clipper + - cshl_fastx_trimmer + update_time: '2014-12-04' + versions: 1 +- create_time: '2014-11-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4aad96570d252f95 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4aad96570d252f95 + name: ChIP-seq control hg38, create BAM for control samples (INPUT, IgG, etc.) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie_wrapper + - sam_to_bam + - samtools_flagstat + - samtools_rmdup + update_time: '2014-12-01' + versions: 0 +- create_time: '2014-11-24' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 846b6fa2b8e20c3c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=846b6fa2b8e20c3c + name: RNA-Seq Mapping + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - tophat2 + - cufflinks + update_time: '2014-11-25' + versions: 2 +- create_time: '2014-11-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: dcb73fce390b36b2 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=dcb73fce390b36b2 + name: ChIP-seq workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie_wrapper + - peakcalling_macs + - fastq_stats + update_time: '2014-11-25' + versions: 2 +- create_time: '2014-11-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4da3871ed87e8f21 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4da3871ed87e8f21 + name: SNP calls (bwa-unified genotyper) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bwa_wrapper + - gatk_unified_genotyper + - sam_to_bam + update_time: '2014-11-25' + versions: 0 +- create_time: '2014-11-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: bad9b88a6d5b6759 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=bad9b88a6d5b6759 + name: Kumova Problem Set + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - naive_variant_caller + - fastq_groomer + - bwa_wrapper + - bedtools_genomecoveragebed_histogram + update_time: '2014-11-04' + versions: 0 +- create_time: '2014-10-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 433a71f7f2d17834 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=433a71f7f2d17834 + name: Coding Exons with the largest number of Simple Repeats + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - sort1 + update_time: '2014-10-26' + versions: 0 +- create_time: '2014-10-22' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: c3b3b2ee14bbd374 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c3b3b2ee14bbd374 + name: Workflow constructed from history 'TP Galaxy' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gatk_depth_of_coverage + - picard_ARRG + - rgPicardMarkDups + - gatk_variant_eval + - bwa_wrapper + - sam_to_bam + - fastq_groomer + - gatk_unified_genotyper + - createInterval + update_time: '2014-10-22' + versions: 0 +- create_time: '2014-10-13' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: eb20150175a6ab03 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=eb20150175a6ab03 + name: Workflow constructed from history 'GALAXY workshop' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bowtie_wrapper + - sam_bw_filter + - samtools_mpileup + - sam_to_bam + - fastq_groomer + - fastq_trimmer + update_time: '2014-10-13' + versions: 1 +- create_time: '2014-10-13' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 1b385fd45ee48614 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=1b385fd45ee48614 + name: Workflow constructed from history 'galaxyWorkshop' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bowtie_wrapper + - sam_bw_filter + - samtools_mpileup + - sam_pileup + - sam_to_bam + - fastq_groomer + - fastq_trimmer + update_time: '2014-10-13' + versions: 2 +- create_time: '2014-02-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 173def229790fbee + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=173def229790fbee + name: SNP calls analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bwa_wrapper + - gatk_unified_genotyper + - sam_to_bam + update_time: '2014-09-30' + versions: 1 +- create_time: '2014-09-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b11171cc4ccd84c7 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=b11171cc4ccd84c7 + name: Galaxy 101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2014-09-11' + versions: 3 +- create_time: '2014-09-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 77a1a9e7dc414650 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=77a1a9e7dc414650 + name: linkY - discover Y-linked genes from RNASeq data; testtoolshed.g2.bx.psu.edu/view/biomonika/linkyx + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rgPicardMarkDups + - trinityrnaseq + - samtools_sort + - bwa_wrapper + - LINKYX_Y + - cat1 + - sam_to_bam + - reformat_trinity_header + - fastq_groomer + update_time: '2014-09-10' + versions: 0 +- create_time: '2014-09-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f895ed9fb68d3379 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f895ed9fb68d3379 + name: linkX - discover X-linked genes from RNASeq data; testtoolshed.g2.bx.psu.edu/view/biomonika/linkyx + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rgPicardMarkDups + - trinityrnaseq + - samtools_sort + - bwa_wrapper + - LINKYX_mpileup + - LINKYX_X + - sam_to_bam + - reformat_trinity_header + - fastq_groomer + update_time: '2014-09-10' + versions: 0 +- create_time: '2014-09-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5de035c08af915ea + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=5de035c08af915ea + name: 'copy: paired w/out candidates (MOD)' + number_of_steps: null + source: https://usegalaxy.org + tags: + - fastq + - paired-end + - formatting + tools: + - join1 + - fastq_to_tabular + - addValue + - comp1 + - tabular_to_fastq + update_time: '2014-09-09' + versions: 0 +- create_time: '2014-03-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: dd4b22d90680beb0 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=dd4b22d90680beb0 + name: testing 'Genotyper (takes BAM, makes VCF)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpSift_filter + - gatk_unified_genotyper + update_time: '2014-09-04' + versions: 1 +- create_time: '2014-08-20' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 4a5730954d776cb2 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4a5730954d776cb2 + name: 'imported: CloudMap_Unmapped_Mutant_Worklfow_single ends' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gatk_depth_of_coverage + - picard_ARRG + - rgPicardMarkDups + - snpSift_filter + - gatk_variant_select + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - sam_to_bam + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - Filter1 + update_time: '2014-08-20' + versions: 0 +- create_time: '2009-08-26' + creators: [] + doi: '' + edam_operation: + - ID mapping + - Phylogenetic tree visualisation + - Database search + edam_topic: [] + id: 55aa743125c2465d + latest_version: 14 + license: null + link: https://usegalaxy.org/published/workflow?id=55aa743125c2465d + name: otu relabelled analysis + number_of_steps: null + source: https://usegalaxy.org + tags: + - metagenomics + - galaxy + - NGS + - Metagenomics + tools: + - t2t_report + - lca1 + - megablast_wrapper + - fasta2tab + - join1 + - cat1 + - Fetch Taxonomic Ranks + - tab2fasta + - Draw_phylogram + - trim_reads + - addValue + - Filter1 + - fasta_compute_length + update_time: '2014-08-20' + versions: 14 +- create_time: '2014-07-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4c6497b245d9c414 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4c6497b245d9c414 + name: Rnbeads + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2014-07-01' + versions: 0 +- create_time: '2014-06-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a808c139402d7b87 + latest_version: 16 + license: null + link: https://usegalaxy.org/published/workflow?id=a808c139402d7b87 + name: Fasta labeled by identifiers + number_of_steps: null + source: https://usegalaxy.org + tags: + - fasta + - reformat + - identifiers + - datasets + tools: + - fasta2tab + - tab2fasta + - cshl_fasta_formatter + update_time: '2014-06-26' + versions: 16 +- create_time: '2014-01-05' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Formatting + - Sequencing quality control + edam_topic: [] + id: b2176abeb937f026 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=b2176abeb937f026 + name: RNAseq with rRNA removal MED4 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastx_clipper + - comp1 + - bowtie_wrapper + - sam_bw_filter + - subtract_query1 + - sam_to_bam + - cshl_fastx_trimmer + - picard_SamToFastq + - fastq_groomer + update_time: '2014-06-23' + versions: 3 +- create_time: '2014-06-18' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 67c2ca24bc0be58e + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=67c2ca24bc0be58e + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_groomer + - bowtie2 + update_time: '2014-06-19' + versions: 1 +- create_time: '2014-06-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a8df35c2754f2aa3 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a8df35c2754f2aa3 + name: MGEScan - identifying long terminal repeats (LTR) and non-LTR retroelements + in eukaryotic genomic sequences + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - find-ltr + - repeatmasker + - mgescan-nonltr + - ltr-gff + - ltr-preprocessing-scaffold + update_time: '2014-06-17' + versions: 0 +- create_time: '2014-01-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 72f92e14f4b61c68 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=72f92e14f4b61c68 + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - rgPicardMarkDups + - gatk_indel_realigner + - bwa_wrapper + - gatk_realigner_target_creator + - gatk_unified_genotyper + update_time: '2014-06-15' + versions: 1 +- create_time: '2014-03-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e77c09c72dfaa9a4 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=e77c09c72dfaa9a4 + name: Subtracting strains from VCF uwml + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + - gatk_variant_select + update_time: '2014-06-03' + versions: 3 +- create_time: '2014-03-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cb153c8d1685de3b + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=cb153c8d1685de3b + name: VCF to snpeffs uwml + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + update_time: '2014-06-03' + versions: 4 +- create_time: '2014-05-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9cc814d43379c2a6 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6 + name: Workflow constructed from history 'Extract Workflow' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Count1 + - Add_a_column1 + - XY_Plot_1 + - Grouping1 + - histogram_rpy + - Filter1 + - gops_coverage_1 + update_time: '2014-05-13' + versions: 3 +- create_time: '2013-12-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e4f6b68301aafd38 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=e4f6b68301aafd38 + name: Workflow constructed from history 'Tutorial (Yodosha, 2014)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - gops_intersect_1 + - Cut1 + update_time: '2014-05-08' + versions: 3 +- create_time: '2014-04-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f55eef988605523e + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f55eef988605523e + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2014-05-07' + versions: 0 +- create_time: '2014-05-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 67080f040e855990 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=67080f040e855990 + name: Genome Coverage Histogram + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + - bedtools_genomecoveragebed_histogram + - Add_a_column1 + - XY_Plot_1 + - Grouping1 + - cat1 + - Grep1 + - Show beginning1 + update_time: '2014-05-06' + versions: 0 +- create_time: '2014-04-19' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 02d49c5f0d9aa010 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=02d49c5f0d9aa010 + name: HW5(Huvec) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bwa_wrapper + - PicardASMetrics + - sam_to_bam + - cshl_fastq_quality_filter + - cshl_fastx_artifacts_filter + - fastq_groomer + update_time: '2014-04-29' + versions: 1 +- create_time: '2014-04-18' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 8356ee639055cbca + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=8356ee639055cbca + name: HW5(GM20000) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bwa_wrapper + - PicardASMetrics + - sam_to_bam + - cshl_fastq_quality_filter + - cshl_fastx_artifacts_filter + - fastq_groomer + - fastq_trimmer + update_time: '2014-04-29' + versions: 1 +- create_time: '2014-04-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 244cf7723892cac4 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=244cf7723892cac4 + name: HW5(2) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sam_merge2 + - peakcalling_macs + update_time: '2014-04-29' + versions: 4 +- create_time: '2014-04-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4be28cd3b398e0d6 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=4be28cd3b398e0d6 + name: Homework 4 part 2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sam_merge2 + - peakcalling_macs + update_time: '2014-04-29' + versions: 3 +- create_time: '2014-03-27' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: b9e3676a84b7be5d + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=b9e3676a84b7be5d + name: HW5 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bwa_wrapper + - PicardASMetrics + - sam_to_bam + - fastq_groomer + update_time: '2014-04-29' + versions: 7 +- create_time: '2014-03-25' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 4703371e94b67347 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=4703371e94b67347 + name: Homework 5 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - bwa_wrapper + - PicardASMetrics + - sam_to_bam + - fastq_groomer + update_time: '2014-04-29' + versions: 8 +- create_time: '2014-04-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6471aa8abbb3fa40 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=6471aa8abbb3fa40 + name: HW5-Fetch + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - flanking_features_1 + - Cut1 + update_time: '2014-04-25' + versions: 2 +- create_time: '2014-04-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a1333d6d9af28547 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a1333d6d9af28547 + name: Workflow constructed from history 'Exercise 1' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - Summary_Statistics1 + - Filter1 + update_time: '2014-04-22' + versions: 0 +- create_time: '2012-01-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 013bf76cb3a8bd66 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=013bf76cb3a8bd66 + name: 'imported: Constructed Workflow_tests_lj' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_intersect_1 + - get_flanks1 + update_time: '2014-03-27' + versions: 2 +- create_time: '2014-03-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0b3af7e9ac69a6b7 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7 + name: workflow2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - bowtie_wrapper + - samtools_mpileup + - sam_to_bam + - pileup_interval + - samtools_flagstat + - fastq_groomer + update_time: '2014-03-25' + versions: 3 +- create_time: '2014-03-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 378159d1ad2e98f9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=378159d1ad2e98f9 + name: FastQ Filter, Sort BAM + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - sam_bw_filter + - sam_to_bam + update_time: '2014-03-19' + versions: 0 +- create_time: '2010-12-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1e2e064c33b9c521 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=1e2e064c33b9c521 + name: trial experiment + number_of_steps: null + source: https://usegalaxy.org + tags: + - rna + - seq + - sam + - paired + - unique + tools: + - sort1 + - sam_bw_filter + - Grouping1 + - comp1 + - Filter1 + update_time: '2014-03-19' + versions: 7 +- create_time: '2014-03-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a7a145c196aa55c9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=a7a145c196aa55c9 + name: Exome Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: + - Exome + - exome + - exome + - workflow + tools: + - rgPicardMarkDups + - bwa_wrapper + - vcftools_annotate + - sam_to_bam + - table_annovar + - samtools_flagstat + - Filter1 + - samtools_mpileup + - varscan + update_time: '2014-03-17' + versions: 0 +- create_time: '2014-02-08' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 83fbcdf3e29c41d0 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=83fbcdf3e29c41d0 + name: 'unified genotyper on ''imported: CloudMap Variant Discovery Mapping (and + Variant Calling) workflow _2-7-2014''' + number_of_steps: null + source: https://usegalaxy.org + tags: + - variant-calling + tools: + - fastqc + - gatk_depth_of_coverage + - picard_ARRG + - rgPicardMarkDups + - gatk_variant_select + - snpSift_filter + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - check_snpeff_candidates + - sam_to_bam + - cloudmap_variant_discovery_mapping + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - Filter1 + update_time: '2014-03-05' + versions: 0 +- create_time: '2014-02-08' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: ea817818a6de77e0 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ea817818a6de77e0 + name: 2016_09_05_FB_script_playground_2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - gatk_depth_of_coverage + - picard_ARRG + - rgPicardMarkDups + - gatk_variant_select + - snpSift_filter + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - check_snpeff_candidates + - sam_to_bam + - cloudmap_variant_discovery_mapping + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - snp_mapping_using_wgs + - Filter1 + update_time: '2014-03-05' + versions: 0 +- create_time: '2014-02-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: eae740bac11ecc91 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=eae740bac11ecc91 + name: diff & merge of 'tophat & cufflinks' (PE vs Non-PE) + number_of_steps: null + source: https://usegalaxy.org + tags: + - nascent + - RNA + tools: + - cufflinks + - cuffcompare + - cuffmerge + - tophat + update_time: '2014-02-23' + versions: 4 +- create_time: '2013-11-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5dfeddb993c2849c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=5dfeddb993c2849c + name: NGS_SAM + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bcftools_view + - samtools_mpileup + update_time: '2014-02-18' + versions: 1 +- create_time: '2012-04-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 77bafc76065c848a + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=77bafc76065c848a + name: Sort BAM preserving headers + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - bam_to_sam + - cat1 + - Grep1 + - sam_to_bam + update_time: '2014-02-18' + versions: 3 +- create_time: '2014-02-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f1dd64a7464054a4 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f1dd64a7464054a4 + name: 'Jeremy: Tophat fusion post output to chrint' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - Cut1 + update_time: '2014-02-11' + versions: 0 +- create_time: '2013-12-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - ID mapping + - Sequence composition calculation + - Database search + - Sequencing quality control + edam_topic: [] + id: fe3d4001499c3f15 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=fe3d4001499c3f15 + name: v-siRNA Extractor + number_of_steps: null + source: https://usegalaxy.org + tags: + - virus + - viroid + - illumina + - sRNAs + tools: + - fastqc + - sort1 + - Count1 + - fastq_filter + - cshl_fastx_clipper + - Cut1 + - bowtie_wrapper + - bam_to_sam + - Fetch Taxonomic Ranks + - Convert characters1 + - CONVERTER_sam_to_bam + - cshl_fastx_artifacts_filter + - fastq_groomer + update_time: '2014-02-04' + versions: 1 +- create_time: '2014-02-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - ID mapping + - Sequence composition calculation + - Read mapping + - Database search + - Sequencing quality control + edam_topic: [] + id: 02c9244e2fb060de + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=02c9244e2fb060de + name: v-siRNA Extractor_2 + number_of_steps: null + source: https://usegalaxy.org + tags: + - illumina + - virus + - sirnas + - viroid + tools: + - fastqc + - sort1 + - Count1 + - fastq_filter + - cshl_fastx_clipper + - Cut1 + - cshl_fastx_artifacts_filter + - bam_to_sam + - sam2interval + - cat1 + - Grep1 + - Convert characters1 + - Fetch Taxonomic Ranks + - CONVERTER_Bam_Bai_0 + - CONVERTER_sam_to_bam + - fastq_groomer + - bowtie2 + update_time: '2014-02-03' + versions: 0 +- create_time: '2013-07-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4ca3b9bb720e9233 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=4ca3b9bb720e9233 + name: Galaxy101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2014-01-21' + versions: -1 +- create_time: '2014-01-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e73a5cf64bd4a372 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e73a5cf64bd4a372 + name: Unnamed workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2014-01-16' + versions: 0 +- create_time: '2013-12-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 65cc7722fb5d626a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=65cc7722fb5d626a + name: Shortened CloudMap Variant Discovery Mapping (Subtracts Crossing Strain from + List of Homozygous and Heterozygous Variants called by GATK Unified Genotyper + default settings)_12-22-2013 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cloudmap_variant_discovery_mapping + - gatk_variant_select + update_time: '2013-12-21' + versions: 0 +- create_time: '2013-06-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 25903aa8a238222d + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=25903aa8a238222d + name: CloudMap Variant Discovery Mapping (Subtracts Crossing Strain from List of + Homozygous and Heterozygous Variants called by GATK Unified Genotyper default + settings)_12-21-2013 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cloudmap_variant_discovery_mapping + - gatk_variant_select + update_time: '2013-12-21' + versions: 3 +- create_time: '2013-08-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b48ff652fc8fbee2 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=b48ff652fc8fbee2 + name: Sort SAM file for Cufflinks + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - cat1 + - Grep1 + update_time: '2013-12-06' + versions: -1 +- create_time: '2013-11-18' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 035c28a247976f2c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=035c28a247976f2c + name: 'imported: Differential gene expression for zebrafish RNA-seq$good$' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sort1 + - cufflinks + - cuffdiff + - tophat + - cuffmerge + - fastq_groomer + update_time: '2013-11-19' + versions: 1 +- create_time: '2013-10-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4769befb88f653d6 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=4769befb88f653d6 + name: Create MEME-ChIP input FASTA file (100bp center regions) from BED6 file + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - Cut1 + - Extract genomic DNA 1 + update_time: '2013-10-28' + versions: 3 +- create_time: '2013-10-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 28e86ab943c67417 + latest_version: 24 + license: null + link: https://usegalaxy.org/published/workflow?id=28e86ab943c67417 + name: Create MEME-ChIP input FASTA file (500bp summit regions) from ENCODE narrowpeak + file. + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - Cut1 + - Extract genomic DNA 1 + update_time: '2013-10-19' + versions: 24 +- create_time: '2013-10-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ea97d3a23e6d38e6 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ea97d3a23e6d38e6 + name: map knownGene to KEGG + number_of_steps: null + source: https://usegalaxy.org + tags: + - KEGG + - pathway + - gene + - mapping + - human + tools: + - join1 + - Remove beginning1 + - Cut1 + update_time: '2013-10-14' + versions: 0 +- create_time: '2013-09-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 295f4687454081be + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=295f4687454081be + name: Panda_Gene_Mapping_Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_flagstat + - CONVERTER_sam_to_bam + - fastq_groomer + - bwa_wrapper + update_time: '2013-09-18' + versions: -1 +- create_time: '2013-09-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f2465afbdfc8ad46 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f2465afbdfc8ad46 + name: Panda_Gene_Mapping_Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - samtools_flagstat + - CONVERTER_sam_to_bam + - fastq_groomer + - bwa_wrapper + update_time: '2013-09-18' + versions: 0 +- create_time: '2013-09-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 642cad26f766339b + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=642cad26f766339b + name: MACS1.3 peaks bed file correction + number_of_steps: null + source: https://usegalaxy.org + tags: + - ChIP + - MACS + tools: + - Add_a_column1 + - Grep1 + - Remove beginning1 + - Cut1 + update_time: '2013-09-10' + versions: 0 +- create_time: '2013-08-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b9986a0f2ecb453a + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=b9986a0f2ecb453a + name: Sort SAM file for Cufflinks + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - cat1 + - Grep1 + update_time: '2013-08-12' + versions: -1 +- create_time: '2012-04-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 85637c4857d97929 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=85637c4857d97929 + name: Sort BAM + number_of_steps: null + source: https://usegalaxy.org + tags: + - BAM + tools: + - sort1 + - bam_to_sam + - sam_to_bam + update_time: '2013-08-07' + versions: 1 +- create_time: '2013-08-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8d3557a82f49528c + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=8d3557a82f49528c + name: AD Fastq joiner QC- splitter - Input Datasets + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_paired_end_joiner + update_time: '2013-08-03' + versions: -1 +- create_time: '2013-07-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 138311394c077827 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=138311394c077827 + name: Workflow 'Add_LinkOut_UCSC_hg18_to_C9-BED' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - addValue + - Convert characters1 + - Cut1 + - mergeCols1 + update_time: '2013-07-30' + versions: 0 +- create_time: '2013-07-23' + creators: [] + doi: '' + edam_operation: + - Formatting + edam_topic: [] + id: 69bb44cd732a0c49 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=69bb44cd732a0c49 + name: 3 conditions, 2 reps + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + - Illumina + - Tophat + - Cuffdiff + tools: + - sam_merge2 + - picard_ReorderSam + - cuffdiff + - tophat + - bedtools_genomecoveragebed_bedgraph + - samtools_flagstat + - wig_to_bigWig + update_time: '2013-07-23' + versions: 3 +- create_time: '2013-07-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b62535ba597d3323 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b62535ba597d3323 + name: Shared_bioblend + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2013-07-19' + versions: 0 +- create_time: '2013-07-17' + creators: [] + doi: '' + edam_operation: + - Formatting + edam_topic: [] + id: b6c0208e49cd2271 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b6c0208e49cd2271 + name: off targets + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Count1 + - bam_to_sam + - fastq_to_tabular + - picard_SamToFastq + - cshl_fastq_quality_filter + - Filter1 + update_time: '2013-07-17' + versions: 0 +- create_time: '2013-05-15' + creators: [] + doi: '' + edam_operation: + - Formatting + edam_topic: [] + id: 46f8999f91221fed + latest_version: 9 + license: null + link: https://usegalaxy.org/published/workflow?id=46f8999f91221fed + name: RNA-seq differential analysis (single-end short reads, 2 conditions, 3 replicates) + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + - Illumina + - Tophat + - Cuffdiff + tools: + - sam_merge2 + - picard_ReorderSam + - cuffdiff + - tophat + - bedtools_genomecoveragebed_bedgraph + - samtools_flagstat + - wig_to_bigWig + update_time: '2013-07-17' + versions: 9 +- create_time: '2013-07-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 30507545aa971637 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=30507545aa971637 + name: Splice site analysis (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - gops_intersect_1 + - cat1 + - addValue + - Filter1 + - Extract genomic DNA 1 + update_time: '2013-07-09' + versions: -1 +- create_time: '2012-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 55911cad792d4f59 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=55911cad792d4f59 + name: 1 peak and more + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - gops_join_1 + - join1 + - Grouping1 + - cat1 + - addValue + - Filter1 + update_time: '2013-07-04' + versions: 2 +- create_time: '2012-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3a172bd71ea15178 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=3a172bd71ea15178 + name: 5 peaks-result + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - cat1 + - addValue + - Filter1 + update_time: '2013-07-04' + versions: 1 +- create_time: '2012-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 81c0d753e90df858 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=81c0d753e90df858 + name: 5 peaks and more + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - join1 + - Grouping1 + - addValue + - Filter1 + update_time: '2013-07-04' + versions: 2 +- create_time: '2012-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d6d49e6c823e7d54 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=d6d49e6c823e7d54 + name: 'imported: 4 peaks-result' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - cat1 + - addValue + - Filter1 + update_time: '2013-07-04' + versions: 2 +- create_time: '2012-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2b298d673d93309d + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=2b298d673d93309d + name: 4 peaks and more + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - join1 + - Grouping1 + - addValue + - Filter1 + update_time: '2013-07-04' + versions: 4 +- create_time: '2012-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f6ee07c7edf170fb + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=f6ee07c7edf170fb + name: 3 peaks-result + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - cat1 + - addValue + - Filter1 + update_time: '2013-07-04' + versions: 2 +- create_time: '2012-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e0da87cadb1e6d5f + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=e0da87cadb1e6d5f + name: 2 peaks-result + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - cat1 + - addValue + - Filter1 + update_time: '2013-07-04' + versions: 4 +- create_time: '2012-04-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a0bffeb8cc263a5b + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=a0bffeb8cc263a5b + name: 3 peaks and more + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - join1 + - Grouping1 + - addValue + - Filter1 + update_time: '2013-07-04' + versions: 3 +- create_time: '2013-06-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a4bda96bae17d039 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a4bda96bae17d039 + name: v2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cloudmap_variant_discovery_mapping + - gatk_variant_select + update_time: '2013-06-27' + versions: 1 +- create_time: '2013-06-04' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7253824f78a90431 + latest_version: 11 + license: null + link: https://usegalaxy.org/published/workflow?id=7253824f78a90431 + name: GSE37764 fastq to bam + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - tophat + - fastq_groomer + - fastq_quality_trimmer + update_time: '2013-06-13' + versions: 11 +- create_time: '2013-05-15' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: cd14df23bb05db2c + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=cd14df23bb05db2c + name: Preproc and TH + number_of_steps: null + source: https://usegalaxy.org + tags: + - RNAseq + - illumina + tools: + - fastqc + - fastq_groomer + - fastq_quality_trimmer + - cshl_fastx_clipper + update_time: '2013-06-03' + versions: 5 +- create_time: '2013-05-28' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: f823b87dd06ba4ac + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac + name: From the beginning (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sam_merge2 + - fastqc + - bowtie_wrapper + - sam_to_bam + - histogram_rpy + - samtools_flagstat + - fastq_paired_end_splitter + - Filter1 + update_time: '2013-05-28' + versions: 3 +- create_time: '2013-05-28' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d2864aa3631b3bf6 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=d2864aa3631b3bf6 + name: From the beginning + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - sam_merge2 + - bowtie_wrapper + - sam_to_bam + - histogram_rpy + - samtools_flagstat + - Filter1 + update_time: '2013-05-28' + versions: 1 +- create_time: '2013-04-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3edea70fbdb9dbd9 + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=3edea70fbdb9dbd9 + name: methratio -g option + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - cat1 + - trimmer + - Filter1 + update_time: '2013-04-19' + versions: 13 +- create_time: '2013-03-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 79454a1e3fe171de + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=79454a1e3fe171de + name: Workflow constructed from history 'Test History 15' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Show beginning1 + update_time: '2013-04-19' + versions: 3 +- create_time: '2013-03-04' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 712d9ae42b45c4b9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=712d9ae42b45c4b9 + name: Workflow constructed from history 'MMBIO 662 Udall 2013' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cuffcompare + - cufflinks + - cuffdiff + - tophat + - fastq_quality_trimmer + - cuffmerge + - fastq_groomer + update_time: '2013-04-19' + versions: 0 +- create_time: '2012-03-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e5c066644cc7cc07 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=e5c066644cc7cc07 + name: Workflow 2 & 3 GAL + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - join1 + - Grouping1 + - cat1 + - addValue + - Filter1 + update_time: '2013-04-02' + versions: 3 +- create_time: '2013-04-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c88708cd216dbc17 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=c88708cd216dbc17 + name: Workflow 2 & 3 GAL + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - join1 + - Grouping1 + - cat1 + - addValue + - Filter1 + update_time: '2013-04-02' + versions: -1 +- create_time: '2013-03-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 85c3a1fc1d3d3df8 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8 + name: small RNA + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_filter + - cshl_fastx_clipper + - bowtie_wrapper + - sam_to_bam + - fastq_groomer + update_time: '2013-03-20' + versions: -1 +- create_time: '2013-03-18' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 0599241ce8eae217 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=0599241ce8eae217 + name: ngs-workshop-dm3ch4 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cuffdiff + - fastq_groomer + - tophat + update_time: '2013-03-18' + versions: 0 +- create_time: '2013-01-28' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 77e4bb9d6aea0c9a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=77e4bb9d6aea0c9a + name: Full + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cshl_fastx_clipper + - cuffdiff + - tophat + - fastq_groomer + update_time: '2013-03-15' + versions: 0 +- create_time: '2013-01-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f25a3da4b00eddbb + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb + name: SampleAnna + number_of_steps: null + source: https://usegalaxy.org + tags: + - intervals + - bedtools + - slop + tools: + - gops_merge_1 + - gops_concat_1 + - get_flanks1 + update_time: '2013-03-15' + versions: 2 +- create_time: '2012-02-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 34ed5c1ceeed43c1 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=34ed5c1ceeed43c1 + name: Workflow 1 (PLUS version) ETU + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - bwa_wrapper + - sam_bw_filter + - sam_pileup + - cat1 + - Grep1 + - sam_to_bam + update_time: '2013-03-07' + versions: 0 +- create_time: '2013-02-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b4dda054d2cf15b7 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=b4dda054d2cf15b7 + name: 'imported: CloudMap Hawaiian Variant Mapping with WGS and Variant Calling + workflow (no candidate genes)_single read' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - fastq_stats + - picard_ARRG + - rgPicardMarkDups + - gatk_variant_select + - snpSift_filter + - gatk_indel_realigner + - snp_mapping_using_wgs + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - sam_to_bam + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - qual_stats_boxplot + - Filter1 + update_time: '2013-02-25' + versions: -1 +- create_time: '2013-02-16' + creators: [] + doi: '' + edam_operation: + - ID mapping + - Phylogenetic tree visualisation + - Database search + edam_topic: [] + id: 59347cc210c4cdbc + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc + name: otu relabelled analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - t2t_report + - lca1 + - megablast_wrapper + - fasta2tab + - join1 + - cat1 + - Fetch Taxonomic Ranks + - tab2fasta + - Draw_phylogram + - trim_reads + - addValue + - Filter1 + - fasta_compute_length + update_time: '2013-02-16' + versions: -1 +- create_time: '2013-02-11' + creators: [] + doi: '' + edam_operation: + - ID mapping + - Phylogenetic tree visualisation + - Database search + edam_topic: [] + id: 19c9c8cc3c813bda + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda + name: otu relabelled analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - t2t_report + - lca1 + - megablast_wrapper + - fasta2tab + - join1 + - cat1 + - Fetch Taxonomic Ranks + - tab2fasta + - Draw_phylogram + - trim_reads + - addValue + - Filter1 + - fasta_compute_length + update_time: '2013-02-11' + versions: -1 +- create_time: '2013-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 29a80db9f3208c29 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=29a80db9f3208c29 + name: miRNA Mapping and DE + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cshl_fastx_clipper + - bowtie_wrapper + - cuffdiff + - sam_to_bam + - fastq_groomer + update_time: '2013-01-29' + versions: 1 +- create_time: '2013-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0115daec07bb1da6 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=0115daec07bb1da6 + name: RTTS Mapper + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Count1 + - Add_a_column1 + - sam2interval + - cat1 + - Grep1 + - subtract_query1 + - Filter1 + update_time: '2013-01-29' + versions: 2 +- create_time: '2013-01-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f8238234db6f04c3 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=f8238234db6f04c3 + name: handson + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - Show beginning1 + update_time: '2013-01-12' + versions: 0 +- create_time: '2012-12-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4782a4943b6fa990 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4782a4943b6fa990 + name: ChIP-Seq analysis on BAM files + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - peakcalling_macs + - CONVERTER_bed_to_genetrack_0 + - build_ucsc_custom_track_1 + update_time: '2012-12-19' + versions: 0 +- create_time: '2012-12-14' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 462261c5e22635f0 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=462261c5e22635f0 + name: Dylan W Scott - Genomics Galaxy Exercise + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - cufflinks + - cuffdiff + - tophat + - CONVERTER_interval_to_bed6_0 + - cuffmerge + - CONVERTER_bed_to_genetrack_0 + - CONVERTER_interval_to_bedstrict_0 + - fastq_trimmer + update_time: '2012-12-17' + versions: 0 +- create_time: '2012-12-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7f835da4ef3b57c8 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=7f835da4ef3b57c8 + name: Analysis1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - comp1 + - Filter1 + update_time: '2012-12-17' + versions: 2 +- create_time: '2012-06-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 96981d6acd91dc03 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=96981d6acd91dc03 + name: 'imported: MACS (mm8)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - peakcalling_macs + - fastq_groomer + - bwa_wrapper + - sam_to_bam + update_time: '2012-12-12' + versions: 2 +- create_time: '2012-12-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 41b181f1d763e419 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=41b181f1d763e419 + name: Index Separation-FASTQ-Tophat + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_manipulation + - tophat + - tabular_to_fastq + - Filter1 + update_time: '2012-12-07' + versions: -1 +- create_time: '2012-12-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5bc973dd30f22525 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=5bc973dd30f22525 + name: Merging and sorting reads + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Count1 + - Paste1 + - mergeCols1 + update_time: '2012-12-07' + versions: -1 +- create_time: '2012-12-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e3c1736cca484dda + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e3c1736cca484dda + name: BamCoveragePlot + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - XY_Plot_1 + - gops_intersect_1 + - sam_pileup + - cat1 + - Convert characters1 + - Paste1 + - gops_basecoverage_1 + - Filter1 + update_time: '2012-12-06' + versions: 0 +- create_time: '2012-12-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 08ca80ae36c8c576 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=08ca80ae36c8c576 + name: BamExonCoverage1X10X20X30X + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - column_join + - Cut1 + - Add_a_column1 + - Filter1 + - samtools_mpileup + - gops_coverage_1 + update_time: '2012-12-06' + versions: 0 +- create_time: '2012-11-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6f436066dffbc37d + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=6f436066dffbc37d + name: CloudMap Hawaiian Variant Mapping with WGS and Variant Calling workflow - + from BAM new + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - fastq_stats + - picard_ARRG + - rgPicardMarkDups + - gatk_variant_select + - snpSift_filter + - gatk_indel_realigner + - snp_mapping_using_wgs + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - check_snpeff_candidates + - sam_to_bam + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - qual_stats_boxplot + - Filter1 + update_time: '2012-12-03' + versions: -1 +- create_time: '2011-08-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e2fa6584853a0dee + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee + name: Illumina Sequence Prep w/ Trim + number_of_steps: null + source: https://usegalaxy.org + tags: + - illumina + tools: + - fastq_groomer + - fastq_quality_trimmer + - qual_stats_boxplot + - fastq_stats + update_time: '2012-12-03' + versions: 0 +- create_time: '2012-09-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b1cd3f793187d667 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b1cd3f793187d667 + name: 'edited: Cloudmap Uncovered Region Subtraction workflow' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + - gops_subtract_1 + - gops_intersect_1 + update_time: '2012-11-28' + versions: 0 +- create_time: '2012-11-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cf8c6f7742b4f3e6 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=cf8c6f7742b4f3e6 + name: CloudMap Subtract Variants workflow (1 set candidates, 1 sets of variants + to subtract) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - snpEff + - check_snpeff_candidates + - gatk_variant_combine + - gatk_variant_select + update_time: '2012-11-28' + versions: 0 +- create_time: '2012-09-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2b3970d9b28810a1 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=2b3970d9b28810a1 + name: 'imported: CloudMap Unmapped Mutant workflow' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - fastq_stats + - picard_ARRG + - rgPicardMarkDups + - snpSift_filter + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - check_snpeff_candidates + - sam_to_bam + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - qual_stats_boxplot + - Filter1 + update_time: '2012-11-27' + versions: 1 +- create_time: '2012-11-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e35ac40c58953f74 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=e35ac40c58953f74 + name: 'Edited: CloudMap Hawaiian Variant Mapping with WGS and Variant Calling workflow + - FOR SUBREAD' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - fastq_stats + - picard_ARRG + - rgPicardMarkDups + - gatk_variant_select + - snpSift_filter + - gatk_indel_realigner + - snp_mapping_using_wgs + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - check_snpeff_candidates + - sam_to_bam + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - qual_stats_boxplot + - Filter1 + update_time: '2012-11-26' + versions: 6 +- create_time: '2012-10-12' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 400c1d170f073279 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=400c1d170f073279 + name: workflowone + number_of_steps: null + source: https://usegalaxy.org + tags: + - for + tools: + - fastqc + - fasta_compute_length + - fastq_to_fasta_python + update_time: '2012-11-13' + versions: 3 +- create_time: '2012-11-09' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: fcce98489c8ca7a3 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3 + name: 'Workflow constructed from history ''imported: RNAseq analysis''' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastqc + - fastq_trimmer + - cuffcompare + - cufflinks + - cuffdiff + - tophat + - Show beginning1 + update_time: '2012-11-09' + versions: 0 +- create_time: '2012-10-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 055eb85c8ecf0ca3 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=055eb85c8ecf0ca3 + name: Variant subtraction + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - fastq_stats + - picard_ARRG + - rgPicardMarkDups + - snpSift_filter + - gatk_variant_select + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - check_snpeff_candidates + - sam_to_bam + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - qual_stats_boxplot + - Filter1 + update_time: '2012-10-15' + versions: 1 +- create_time: '2012-10-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0017c434354b6f6a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0017c434354b6f6a + name: 'P38-1-op540 imported: CloudMap EMS Variant Density Mapping workflow (takes + VCF of heterozygous and homozygous variants to subtract)' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gatk_depth_of_coverage + - fastq_stats + - picard_ARRG + - rgPicardMarkDups + - snpSift_filter + - gatk_variant_select + - gatk_indel_realigner + - bwa_wrapper + - sam_bw_filter + - bedtools_genomecoveragebed_bedgraph + - check_snpeff_candidates + - sam_to_bam + - ems_variant_density_mapping + - snpEff + - gatk_realigner_target_creator + - gatk_unified_genotyper + - qual_stats_boxplot + - Filter1 + update_time: '2012-10-15' + versions: 1 +- create_time: '2012-10-12' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + edam_topic: [] + id: 8b7e03f09b0183d9 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9 + name: test2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasta_compute_length + - clustalw + - fastq_to_fasta_python + update_time: '2012-10-12' + versions: 1 +- create_time: '2012-07-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a57db139837dd24c + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=a57db139837dd24c + name: Workflow constructed from history 'RNA analysis 1' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffcompare + - fastq_stats + - bowtie_wrapper + - cufflinks + - cuffdiff + - tophat + - sam_bw_filter + - sam_to_bam + - fastq_groomer + - qual_stats_boxplot + update_time: '2012-10-11' + versions: 1 +- create_time: '2012-10-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: fdfe38dc92e51611 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=fdfe38dc92e51611 + name: Convert GFF to bedGraph + number_of_steps: null + source: https://usegalaxy.org + tags: + - bedGraph + - GFF + tools: + - Add_a_column1 + - Cut1 + update_time: '2012-10-10' + versions: 2 +- create_time: '2012-06-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 62401f33a369bac0 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=62401f33a369bac0 + name: RNASeq workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie_wrapper + - cufflinks + - tophat + - bwa_wrapper + - samtools_flagstat + - fastq_groomer + update_time: '2012-09-11' + versions: -1 +- create_time: '2012-08-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8a3e457a9453c313 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=8a3e457a9453c313 + name: Histones_downstream + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - gops_join_1 + - cat1 + - get_flanks1 + update_time: '2012-08-22' + versions: 0 +- create_time: '2012-08-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ebdea787cec2fd72 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=ebdea787cec2fd72 + name: Header to GO Slim + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Convert characters1 + - join1 + update_time: '2012-08-15' + versions: 4 +- create_time: '2012-07-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 61b7ad6588f7db41 + latest_version: 16 + license: null + link: https://usegalaxy.org/published/workflow?id=61b7ad6588f7db41 + name: RNA-Seq_Analysis - 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sam_pileup + - pileup_parser + - bwa_wrapper + - sam_to_bam + update_time: '2011-11-24' + versions: 0 +- create_time: '2010-08-27' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 578f46106f72c971 + latest_version: 25 + license: null + link: https://usegalaxy.org/published/workflow?id=578f46106f72c971 + name: ORIGINAL mt analysis 0.01 strand-specific (fastq double) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - Cut1 + - Add_a_column1 + - bwa_wrapper + - sam_bw_filter + - join1 + - sam_pileup + - cat1 + - Grouping1 + - Grep1 + - sam_to_bam + - addValue + - Filter1 + update_time: '2011-11-18' + versions: 25 +- create_time: '2011-11-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7cae620eea6326af + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=7cae620eea6326af + name: 'Clone of imported: rama proj_tests_lj' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - hyphy_nj_tree_wrapper1 + - Interval_Maf_Merged_Fasta2 + - comp1 + - Interval2Maf1 + - Show beginning1 + - Extract genomic DNA 1 + update_time: '2011-11-16' + versions: 0 +- create_time: '2011-11-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 18395d7c5075edad + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=18395d7c5075edad + name: 'imported: Clone of ''Avinash Workflow - Nov 14th 2011'' shared by ''avinash.banala01@gmail.com_tests_lj' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - CONVERTER_bed_to_genetrack_0 + - CONVERTER_interval_to_bedstrict_0 + - CONVERTER_interval_to_bed6_0 + - CONVERTER_gff_to_bed_0 + update_time: '2011-11-16' + versions: -1 +- create_time: '2011-11-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 857db984ff571191 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=857db984ff571191 + name: linear regression analysis of Genetic Association Studies of Complex Diseases + and Disorders using snps and exons related to them + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_join_1 + - join1 + - LinearRegression1 + - Grouping1 + - scatterplot_rpy + update_time: '2011-11-16' + versions: 0 +- create_time: '2011-11-15' + creators: [] + doi: '' + edam_operation: + - Multiple sequence alignment + edam_topic: [] + id: 7b68f97bf88f99b9 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9 + name: Workflow constructed from history 'Test1' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - hyphy_nj_tree_wrapper1 + - clustalw + update_time: '2011-11-15' + versions: 0 +- create_time: '2011-04-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 66748e20a243eafe + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=66748e20a243eafe + name: Sureselect Find Uncovered Target Intervals + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - gops_subtract_1 + - mergeCols1 + - featureCoverage1 + - addValue + - Filter1 + update_time: '2011-11-14' + versions: 6 +- create_time: '2011-11-13' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9238f7208033d0d6 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=9238f7208033d0d6 + name: ahmedbasudan-chr17project + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_intersect_1 + - join1 + update_time: '2011-11-13' + versions: 2 +- create_time: '2011-08-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8e9882d890ee5ec7 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=8e9882d890ee5ec7 + name: Intersect annotation with 5 partitions(bins) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_intersect_1 + - wc_gnu + update_time: '2011-11-04' + versions: 1 +- create_time: '2011-08-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f806893fbe065406 + latest_version: 5 + license: null + link: https://usegalaxy.org/published/workflow?id=f806893fbe065406 + name: Partition genome into 5 bins based on coverage + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Show tail1 + - Show beginning1 + update_time: '2011-11-04' + versions: 5 +- create_time: '2011-07-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 684ff8ee49c7f116 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=684ff8ee49c7f116 + name: Workflow (single-end, fastq, b37) + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cuffcompare + - fastq_stats + - cufflinks + - cuffdiff + - tophat + - bwa_wrapper + - fastq_groomer + - qual_stats_boxplot + update_time: '2011-11-01' + versions: 8 +- create_time: '2011-09-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4e0ce0ab562f3912 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=4e0ce0ab562f3912 + name: GalaxyTest + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2011-10-24' + versions: 2 +- create_time: '2011-02-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 11dac9cba49be089 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=11dac9cba49be089 + name: Workflow Chrom5 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - Cut1 + - bowtie_wrapper + - sam_pileup + - sam_to_bam + update_time: '2011-10-19' + versions: 3 +- create_time: '2011-09-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 44b27a1296633366 + latest_version: 6 + license: null + link: https://usegalaxy.org/published/workflow?id=44b27a1296633366 + name: Workflow constructed from history 'HGVS & ASHG 2011 SNP Galaxy poster' + number_of_steps: null + source: https://usegalaxy.org + tags: + - SNP + tools: + - ctdBatch_1 + - hgv_sift + - gops_merge_1 + - gops_intersect_1 + - join1 + - mergeCols1 + - Grep1 + - hgv_codingSnps + - addValue + - Filter1 + update_time: '2011-10-14' + versions: 6 +- create_time: '2011-09-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1207eb597775b8a0 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=1207eb597775b8a0 + name: Galaxy101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2011-09-04' + versions: 2 +- create_time: '2011-08-24' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 14206e3899f9ea8a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=14206e3899f9ea8a + name: Sort BAM + number_of_steps: null + source: https://usegalaxy.org + tags: + - MACS + - BAM + - CHiP-seq + tools: + - sort1 + - peakcalling_macs + - bam_to_sam + - sam_to_bam + update_time: '2011-08-25' + versions: 1 +- create_time: '2011-08-02' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 68a9f03d99676bdc + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=68a9f03d99676bdc + name: Make Ensembl GTF compatible with Cufflinks + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - addValue + - Paste1 + - Cut1 + - mergeCols1 + update_time: '2011-08-03' + versions: -1 +- create_time: '2011-05-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4b52f6a8dcfc8045 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=4b52f6a8dcfc8045 + name: 'Clone of ''imported: RNAseq, Part 3_test_lj' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sam2interval + - featureCoverage1 + update_time: '2011-07-26' + versions: 1 +- create_time: '2011-01-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 92a233e5f2405830 + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=92a233e5f2405830 + name: 'imported: RNAseq, Part 2 map to mm9' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie_wrapper + - sam_bw_filter + - sam_to_bam + update_time: '2011-07-26' + versions: 13 +- create_time: '2011-05-11' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6ad3c2d8a14809ca + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=6ad3c2d8a14809ca + name: 'Clone of ''imported: RNAseq, Part 1_tests_lj' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - cshl_fastq_quality_boxplot + - fastq_groomer + - cshl_fastx_quality_statistics + update_time: '2011-07-26' + versions: 0 +- create_time: '2011-07-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b4f04171e8de02ce + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=b4f04171e8de02ce + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fasta2tab + update_time: '2011-07-25' + versions: 0 +- create_time: '2011-07-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 92d0308b5190c4be + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=92d0308b5190c4be + name: Galaxy 101 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2011-07-21' + versions: 0 +- create_time: '2011-05-27' + creators: [] + doi: '' + edam_operation: + - ID mapping + - Phylogenetic tree visualisation + - Database search + edam_topic: [] + id: 2f7638035fb889ac + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=2f7638035fb889ac + name: metagenomic analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - t2t_report + - lca1 + - megablast_wrapper + - fasta2tab + - join1 + - cat1 + - Fetch Taxonomic Ranks + - tab2fasta + - Draw_phylogram + - trim_reads + - addValue + - Filter1 + - fasta_compute_length + update_time: '2011-06-30' + versions: -1 +- create_time: '2011-05-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 38a7b4ca365e96ae + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=38a7b4ca365e96ae + name: 'M1 GMAP: filtros aliniamientos' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - join1 + - Grouping1 + - comp1 + - Filter1 + update_time: '2011-06-29' + versions: 7 +- create_time: '2011-06-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b8742810ac30429d + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=b8742810ac30429d + name: Make Ensembl GTF compatible with Cufflinks + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - addValue + - Paste1 + - Cut1 + - mergeCols1 + update_time: '2011-06-28' + versions: 3 +- create_time: '2011-06-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d860749fd34809d7 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=d860749fd34809d7 + name: miRNA Secondary Analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_filter + - cshl_fastx_clipper + - fastq_to_fasta_python + update_time: '2011-06-21' + versions: 4 +- create_time: '2011-06-14' + creators: [] + doi: '' + edam_operation: + - ID mapping + - Phylogenetic tree visualisation + - Database search + edam_topic: [] + id: 85d825931edf4a64 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=85d825931edf4a64 + name: metagenomic analysis + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - t2t_report + - lca1 + - megablast_wrapper + - fasta2tab + - join1 + - cat1 + - Fetch Taxonomic Ranks + - tab2fasta + - Draw_phylogram + - trim_reads + - addValue + - Filter1 + - fasta_compute_length + update_time: '2011-06-14' + versions: -1 +- create_time: '2011-06-14' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: baf01109a1bf8d0d + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=baf01109a1bf8d0d + name: Overlapping intervals + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_basecoverage_1 + - gops_intersect_1 + update_time: '2011-06-14' + versions: -1 +- create_time: '2011-06-07' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: a666aaaa32f62487 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=a666aaaa32f62487 + name: Fuzznuc.UCSC.Fixithere + number_of_steps: null + source: https://usegalaxy.org + tags: + - fuzznuc + - UCSC + - BED + tools: + - Cut1 + - Add_a_column1 + - 'EMBOSS: fuzznuc37' + - Convert characters1 + - gff2bed1 + - addValue + - Extract genomic DNA 1 + update_time: '2011-06-07' + versions: 7 +- create_time: '2011-05-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 67d79121788892b0 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=67d79121788892b0 + name: fanca + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: [] + update_time: '2011-05-19' + versions: 0 +- create_time: '2011-04-08' + creators: [] + doi: '' + edam_operation: + - Sequence analysis + - Sequence alignment analysis + - Sequence alignment + - Local alignment + - Global alignment + edam_topic: [] + id: 6f836f4b71d399e7 + latest_version: 13 + license: null + link: https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7 + name: 'Clone of ''imported: Sureselect Bin Orphan and High GC Baits_tests_lj' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - 'EMBOSS: geecee41' + - Remove beginning1 + - Cut1 + - Add_a_column1 + - join1 + - gops_cluster_1 + - tab2fasta + - Convert characters1 + - comp1 + - gops_basecoverage_1 + - Filter1 + update_time: '2011-05-05' + versions: 13 +- create_time: '2011-04-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 097b37da08ceca64 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=097b37da08ceca64 + name: 'Compare tables: biostar-7746' + number_of_steps: null + source: https://usegalaxy.org + tags: + - biostar + tools: + - Add_a_column1 + - join1 + - Filter1 + update_time: '2011-04-21' + versions: 0 +- create_time: '2010-10-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c7aca0f5bb660907 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=c7aca0f5bb660907 + name: Prueba Lidia desde original + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - Cut1 + - Add_a_column1 + - bwa_wrapper + - sam_bw_filter + - join1 + - sam_pileup + - cat1 + - Grouping1 + - Grep1 + - sam_to_bam + - addValue + - Filter1 + update_time: '2011-03-24' + versions: 2 +- create_time: '2011-02-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4a9b0534b1c88609 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609 + name: workflow datos 5.1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - bowtie_wrapper + - CONVERTER_bam_to_summary_tree_0 + - cshl_fastx_quality_statistics + - sam_bw_filter + - cshl_fastq_quality_boxplot + - sam_to_bam + - CONVERTER_Bam_Bai_0 + - fastq_groomer + update_time: '2011-03-05' + versions: 0 +- create_time: '2011-02-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 899db1fa0c09130a + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=899db1fa0c09130a + name: Workflow constructed from history 'TRIAL' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gene2exon1 + - sort1 + - Add_a_column1 + - gops_join_1 + - join1 + - Grouping1 + update_time: '2011-03-01' + versions: 1 +- create_time: '2011-02-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 31dea5361ec9421c + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=31dea5361ec9421c + name: restricted Illumina reads to usable SNPs w ref + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - Cut1 + - bowtie_wrapper + - sam_pileup + - sam_to_bam + - fastq_groomer + - Filter1 + update_time: '2011-02-24' + versions: 8 +- create_time: '2011-01-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3479ce3d4a24f7e3 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=3479ce3d4a24f7e3 + name: Sort SAM file for Cufflinks + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - cat1 + - Grep1 + update_time: '2011-01-17' + versions: -1 +- create_time: '2011-01-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3696bd8abe0f7746 + latest_version: -1 + license: null + link: https://usegalaxy.org/published/workflow?id=3696bd8abe0f7746 + name: SOLiD Conversion Mapping for FAIRE + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Count1 + - solid2fastq + - peakcalling_macs + - sam_bw_filter + - bowtie_color_wrapper + update_time: '2011-01-17' + versions: -1 +- create_time: '2010-11-06' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4f02edb5c9bb84ab + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=4f02edb5c9bb84ab + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gops_intersect_1 + - get_flanks1 + update_time: '2010-11-06' + versions: 1 +- create_time: '2010-11-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a019e24e620f51bc + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=a019e24e620f51bc + name: Sort SAM file for Cufflinks + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - cat1 + - Grep1 + update_time: '2010-11-03' + versions: 4 +- create_time: '2010-10-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 6172b57f4c49e364 + latest_version: 20 + license: null + link: https://usegalaxy.org/published/workflow?id=6172b57f4c49e364 + name: SOLiD Conversion Mapping for FAIRE + number_of_steps: null + source: https://usegalaxy.org + tags: + - Convert + - Map + - FAIRE + tools: + - Count1 + - solid2fastq + - peakcalling_macs + - sam_bw_filter + - bowtie_color_wrapper + update_time: '2010-10-27' + versions: 20 +- create_time: '2010-10-25' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 941ced9f12eecd3c + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=941ced9f12eecd3c + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Remove beginning1 + - Cut1 + - join1 + - mergeCols1 + - Grouping1 + - cat1 + - addValue + - Filter1 + update_time: '2010-10-25' + versions: 2 +- create_time: '2010-10-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e107d8036c064616 + latest_version: 10 + license: null + link: https://usegalaxy.org/published/workflow?id=e107d8036c064616 + name: 23 and me chimp + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - Add_a_column1 + - join1 + - Grep1 + - trimmer + - Filter1 + update_time: '2010-10-23' + versions: 10 +- create_time: '2010-10-15' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 468c5a8fe7a40778 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=468c5a8fe7a40778 + name: Chr.22 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - sort1 + - Cut1 + - Add_a_column1 + - Extract genomic DNA 1 + - gops_coverage_1 + - Filter1 + update_time: '2010-10-15' + versions: 0 +- create_time: '2010-09-16' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 58d16d45527990b7 + latest_version: 8 + license: null + link: https://usegalaxy.org/published/workflow?id=58d16d45527990b7 + name: SNP identification within annotated genes from NGS PE Data + number_of_steps: null + source: https://usegalaxy.org + tags: + - snp + - ngs + - pileup + - bowtie + tools: + - pileup_parser + - bowtie_wrapper + - gops_intersect_1 + - sam_pileup + - sam_to_bam + - fastq_groomer + - fastq_trimmer + - Filter1 + update_time: '2010-09-16' + versions: 8 +- create_time: '2010-09-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ab23c641cfdefe0c + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=ab23c641cfdefe0c + name: Test workflow 1 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - fastq_stats + - bowtie_wrapper + - solid_qual_boxplot + - sam_to_bam + - qual_stats_boxplot + update_time: '2010-09-01' + versions: 0 +- create_time: '2010-07-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 478c263e8334bb31 + latest_version: 4 + license: null + link: https://usegalaxy.org/published/workflow?id=478c263e8334bb31 + name: Demo - merging replicates + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Add_a_column1 + - Cut1 + update_time: '2010-07-10' + versions: 4 +- create_time: '2010-07-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c44630305b297933 + latest_version: 3 + license: null + link: https://usegalaxy.org/published/workflow?id=c44630305b297933 + name: Demo - extracting polymorphisms + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Grouping1 + - cat1 + - join1 + - Filter1 + update_time: '2010-07-10' + versions: 3 +- create_time: '2010-06-23' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4339d5625c15ae78 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=4339d5625c15ae78 + name: 'PCR replicate preparation ' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - fastq_stats + - Cut1 + - Add_a_column1 + - gops_join_1 + - bwa_wrapper + - sam_pileup + - cat1 + - Grep1 + - sam_to_bam + - Summary_Statistics1 + - qual_stats_boxplot + - Filter1 + update_time: '2010-06-24' + versions: 0 +- create_time: '2010-06-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 558c28293ec2d239 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=558c28293ec2d239 + name: Mapping replicate with BWA + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - bwa_wrapper + - sam_pileup + - Grep1 + - sam_to_bam + - Summary_Statistics1 + - Filter1 + update_time: '2010-06-24' + versions: 0 +- create_time: '2010-05-20' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 26d2c2d51d6a7158 + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=26d2c2d51d6a7158 + name: duplicate prep BWA -n 2 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - pileup_parser + - Cut1 + - Add_a_column1 + - gops_join_1 + - bwa_wrapper + - sam_bw_filter + - sam_pileup + - cat1 + - Grep1 + - sam_to_bam + - Summary_Statistics1 + - Filter1 + update_time: '2010-06-11' + versions: 0 +- create_time: '2010-06-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 85dc651884b93cf5 + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=85dc651884b93cf5 + name: mRNA SNPs example + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Cut1 + - gops_join_1 + - fasta2tab + - join1 + - Convert characters1 + update_time: '2010-06-08' + versions: 1 +- create_time: '2010-04-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: cad24fc12b2451c6 + latest_version: 7 + license: null + link: https://usegalaxy.org/published/workflow?id=cad24fc12b2451c6 + name: fetching SNP for p1-3 + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Count1 + - Cut1 + - join1 + - cat1 + - Filter1 + update_time: '2010-05-09' + versions: 7 +- create_time: '2010-03-01' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 71621a8a85b93435 + latest_version: 2 + license: null + link: https://usegalaxy.org/published/workflow?id=71621a8a85b93435 + name: my workflow + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - Remove beginning1 + update_time: '2010-03-01' + versions: 2 +- create_time: '2010-02-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 0ef5d77b0f4f9e9f + latest_version: 1 + license: null + link: https://usegalaxy.org/published/workflow?id=0ef5d77b0f4f9e9f + name: test + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - gencode_partition1 + - random_intervals1 + update_time: '2010-02-18' + versions: 1 +- create_time: '2010-01-29' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c6a3b066c3072e4a + latest_version: 0 + license: null + link: https://usegalaxy.org/published/workflow?id=c6a3b066c3072e4a + name: 'imported: SOLiD single end mapping quickie 8' + number_of_steps: null + source: https://usegalaxy.org + tags: [] + tools: + - solid2fastq + - solid_qual_stats + - sam_bw_filter + - sam2interval + - solid_qual_boxplot + - bowtie_color_wrapper + update_time: '2010-02-01' + versions: 0 +- create_time: '2024-10-15' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: aff24131c439dab8 + latest_version: 14 + license: null + link: https://usegalaxy.org.au/published/workflow?id=aff24131c439dab8 + name: Selenium_test_5 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - IO + tools: + - cat1 + - random_lines1 + - jbrowse + update_time: '2024-10-18' + versions: 14 +- create_time: '2024-10-11' + creators: + - Richard Edwards + doi: '' + edam_operation: + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence alignment analysis + - Genome assembly + - Sequence assembly validation + - Scaffolding + edam_topic: [] + id: 0a3fb089674de144 + latest_version: 20 + license: CC-BY-SA-4.0 + link: https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144 + name: Blobtool Plots (HiFi) [v0.1.0] + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Assembly + - HiFi + - Blobtools + - QC + tools: + - bg_diamond + - busco + - blobtoolkit + - minimap2 + update_time: '2024-10-17' + versions: 20 +- create_time: '2024-10-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - SNP detection + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: baa763dbdf6afb71 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=baa763dbdf6afb71 + name: Selenium_test_6 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + tools: + - fastqc + - trimmomatic + - __UNZIP_COLLECTION__ + - vcfvcfintersect + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bwa_mem + - lofreq_call + - __ZIP_COLLECTION__ + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-10-17' + versions: 1 +- create_time: '2023-10-02' + creators: + - Valentine Murigneux, QCIF/Biocommons + doi: '' + edam_operation: + - Statistical calculation + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: a335b9c9103b57ad + latest_version: 116 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad + name: Taxonomy classification using Kraken2 and Bracken + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - shotgun + - GUCFG2Galaxy + - name:Collection + tools: + - Show tail1 + - taxonomy_krona_chart + - collection_element_identifiers + - add_line_to_file + - krakentools_alpha_diversity + - est_abundance + - krakentools_kreport2krona + - cat_multiple + - regex1 + - kraken2 + - Paste1 + - krakentools_combine_kreports + - krakentools_beta_diversity + update_time: '2024-10-15' + versions: 116 +- create_time: '2024-06-12' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 57aa23f4f0418a07 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07 + name: QIIME2-Import_Casava_Paired_End_FastQ + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Amplicon + - QIIME2 + - BGGM + - Microbiome + - PairedReads + tools: + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-10-04' + versions: 1 +- create_time: '2024-10-03' + creators: + - GalaxyP + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: b0a79310e0dc3fb4 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=b0a79310e0dc3fb4 + name: Clinical Metaproteomics Quantitation (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:clinicalMP + tools: + - Grouping1 + - Grep1 + - maxquant + - Cut1 + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: b601f48ecec15bf4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b601f48ecec15bf4 + name: 'COVID-19: variation analysis reporting (release v0.3.4)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-10-03' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: fe5542c99cdc57ce + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=fe5542c99cdc57ce + name: 'COVID-19: variation analysis on ARTIC PE (release v0.5.3)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-10-03' + versions: 1 +- create_time: '2024-09-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - SNP detection + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d35d05be576e8b13 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d35d05be576e8b13 + name: Selenium_test_4 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + tools: + - fastqc + - trimmomatic + - __UNZIP_COLLECTION__ + - vcfvcfintersect + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bwa_mem + - lofreq_call + - __ZIP_COLLECTION__ + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-10-02' + versions: 2 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: 738350fc2ca69c0b + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=738350fc2ca69c0b + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: b09530351a9e9ffb + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b09530351a9e9ffb + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: ccc6602623583bcc + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ccc6602623583bcc + name: RNAseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 56bda8e4b0018e03 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=56bda8e4b0018e03 + name: RNAseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: ce7106593536f900 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ce7106593536f900 + name: ChIPseq_SR (release v0.12) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: fa87a22c8dcd8d78 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=fa87a22c8dcd8d78 + name: ChIPseq_PE (release v0.12) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-26' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2980172ed0226b59 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2980172ed0226b59 + name: CUTandRUN (release v0.13) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-26' + versions: 1 +- create_time: '2024-09-06' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d018214e901419c9 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d018214e901419c9 + name: Selenium_test_2 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + update_time: '2024-09-24' + versions: 1 +- create_time: '2024-09-07' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Antimicrobial resistance prediction + - Genome assembly + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: d78f885b4b86635f + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f + name: Selenium_test_3 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Assembly + - Bacterial + tools: + - fastqc + - fastp + - abricate + - shovill + - fasta-stats + update_time: '2024-09-24' + versions: 1 +- create_time: '2022-04-14' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 9fe99d6a57d51e73 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=9fe99d6a57d51e73 + name: Selenium_test_1 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - bwa_mem + update_time: '2024-09-24' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 543001c51567b438 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=543001c51567b438 + name: 'QIIME2 VI: Diversity metrics and estimations (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - qiime2_core__tools__import + - qiime2__diversity__core_metrics_phylogenetic + - __BUILD_LIST__ + - qiime2__diversity__beta_group_significance + - qiime2__diversity__alpha_group_significance + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 69ad3db9cb0bb3be + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=69ad3db9cb0bb3be + name: QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: [] + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: 131636a795bac485 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=131636a795bac485 + name: Taxonomy Profiling and Visualization with Kron (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - kraken2 + - krakentools_kreport2krona + - taxonomy_krona_chart + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Visualisation + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Mapping + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: b60922a253df6654 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b60922a253df6654 + name: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release + v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - collection_column_join + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - ggplot2_heatmap + - fasta2tab + - tp_replace_in_column + - tp_sorted_uniq + - clustalw + - Remove beginning1 + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - tp_split_on_column + - newick_display + - Count1 + - regexColumn1 + - bedtools_getfastabed + - tp_multijoin_tool + - Cut1 + - fasttree + - tab2fasta + - __FILTER_EMPTY_DATASETS__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - "B\xE9r\xE9nice Batut" + - Engy Nasr + - Paul Zierep + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Visualisation + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: 69d91340fc7effa2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2 + name: Nanopore Preprocessing (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:Nanopore + - name:IWC + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - krakentools_extract_kraken_reads + - collection_column_join + - Cut1 + - collapse_dataset + - Add_a_column1 + - __FILTER_FAILED_DATASETS__ + - bamtools_split_mapped + - regexColumn1 + - kraken2 + - porechop + - Grep1 + - minimap2 + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + edam_topic: [] + id: 084bb76cf47d7060 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060 + name: Gene-based Pathogen Identification (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:PathoGFAIR + - name:IWC + - name:microGalaxy + tools: + - abricate + - medaka_consensus_pipeline + - collection_element_identifiers + - split_file_to_collection + - flye + - fasta2tab + - bandage_image + - tab2fasta + - compose_text_param + - tp_find_and_replace + - __BUILD_LIST__ + - param_value_from_file + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 9016b2be61f89053 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=9016b2be61f89053 + name: Generate Nx and Size plots for multiple assemblies (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - sort1 + - addName + - collapse_dataset + - Add_a_column1 + - Cut1 + - datamash_ops + - gfastats + - param_value_from_file + - tp_awk_tool + - compose_text_param + - ggplot2_point + - addValue + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 2fee25e188531691 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2fee25e188531691 + name: Generate Nx and Size plots for multiple assemblies (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - sort1 + - addName + - collapse_dataset + - Add_a_column1 + - Cut1 + - datamash_ops + - gfastats + - param_value_from_file + - tp_awk_tool + - compose_text_param + - ggplot2_point + - addValue + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: fb517ec08b571a2d + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d + name: 'QIIME2 IIb: Denoising (sequence quality control) and feature table creation + (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - qiime2__feature_table__summarize + - qiime2__feature_table__tabulate_seqs + - qiime2__metadata__tabulate + - qiime2__dada2__denoise_paired + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 2d16ed86414f23b3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3 + name: 'QIIME2 IIa: Denoising (sequence quality control) and feature table creation + (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - qiime2__feature_table__summarize + - qiime2__dada2__denoise_single + - qiime2__feature_table__tabulate_seqs + - qiime2__metadata__tabulate + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: f946d722f7c27479 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479 + name: 'QIIME2 Id: Demultiplexed data (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - collection_element_identifiers + - qiime2__demux__summarize + - qiime2_core__tools__import + - __RELABEL_FROM_FILE__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 3c1bf73067334071 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071 + name: 'QIIME2 Ic: Demultiplexed data (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - collection_element_identifiers + - qiime2__demux__summarize + - qiime2_core__tools__import + - __RELABEL_FROM_FILE__ + - regex1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: 19b0f96df6d09b4e + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e + name: 'QIIME2 Ib: multiplexed data (paired-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - qiime2__demux__emp_paired + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Debjyoti Ghosh + - "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ" + doi: '' + edam_operation: [] + edam_topic: [] + id: cddd668a29b1488a + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a + name: 'QIIME2 Ia: multiplexed data (single-en (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - qiime2__demux__emp_single + - qiime2_core__tools__import + - qiime2__demux__summarize + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Matthias Bernt + - UFZ Leipzig + doi: '' + edam_operation: + - Variant calling + - DNA barcoding + edam_topic: [] + id: 1016f17b77a8216d + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1016f17b77a8216d + name: dada2 amplicon analysis pipeline - for paired en (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:amplicon + tools: + - dada2_makeSequenceTable + - __UNZIP_COLLECTION__ + - dada2_seqCounts + - dada2_assignTaxonomyAddspecies + - dada2_filterAndTrim + - __APPLY_RULES__ + - dada2_mergePairs + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_dada + - dada2_removeBimeraDenovo + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 7168c01be9997823 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=7168c01be9997823 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 543fb2d9431a7e13 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=543fb2d9431a7e13 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: a209f43d8a3cc853 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=a209f43d8a3cc853 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.7) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_grep_tool + - tp_cut_tool + - tp_awk_tool + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 0df25e2dbd5e8ed5 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=0df25e2dbd5e8ed5 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.7.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_grep_tool + - tp_cut_tool + - tp_awk_tool + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 77e0ca6492f40c9c + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=77e0ca6492f40c9c + name: Velocyto-on10X-filtered-barcodes (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - velocyto_cli + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 1e5a77d9e9630115 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1e5a77d9e9630115 + name: Velocyto-on10X-filtered-barcodes (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - velocyto_cli + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 1f1cfa7ee73dfeb2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1f1cfa7ee73dfeb2 + name: Velocyto-on10X-from-bun (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - __APPLY_RULES__ + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: [] + edam_topic: [] + id: 829e193c81642817 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=829e193c81642817 + name: Velocyto-on10X-from-bun (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - __APPLY_RULES__ + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: b88036506d0be117 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b88036506d0be117 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: 0f01e24e6c33a834 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=0f01e24e6c33a834 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - RNA-Seq quantification + edam_topic: [] + id: aa387984ac9e2f71 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=aa387984ac9e2f71 + name: scRNA-seq_preprocessing_10X_cellPlex (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - pick_value + - cite_seq_count + - tp_awk_tool + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: d417e920ff97e4c1 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org.au/published/workflow?id=d417e920ff97e4c1 + name: Assembly-decontamination-VGP9 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: c92fead7c30c7497 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org.au/published/workflow?id=c92fead7c30c7497 + name: Assembly-decontamination-VGP9 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 0edb9c8b767fa74b + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org.au/published/workflow?id=0edb9c8b767fa74b + name: Assembly-decontamination-VGP9 (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - ncbi_blastn_wrapper + - parse_mito_blast + - Filter1 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 8dd86497bc15d981 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=8dd86497bc15d981 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.10) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 319e9d693fac8dce + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=319e9d693fac8dce + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.11) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 5f4f874e49515555 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=5f4f874e49515555 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: c6a71573a299eb3a + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=c6a71573a299eb3a + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 60c0dec52cdca708 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=60c0dec52cdca708 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.2.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - tp_replace_in_line + - Add_a_column1 + - tp_sed_tool + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: ad10cd704268dcf0 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=ad10cd704268dcf0 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 1eb3e1452c672480 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=1eb3e1452c672480 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fe1e7fa0bc437ed8 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=fe1e7fa0bc437ed8 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 371c9892d261cee2 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=371c9892d261cee2 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 87bbf9408b3f2a32 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=87bbf9408b3f2a32 + name: Scaffolding-BioNano-VGP7 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 02f2a556e77eed14 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=02f2a556e77eed14 + name: Scaffolding-BioNano-VGP7 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - tp_find_and_replace + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 141ac7a106e49d8f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=141ac7a106e49d8f + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 049f61f436ff66df + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=049f61f436ff66df + name: kmer-profiling-hifi-VGP1 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 26b57e0b79ea4559 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=26b57e0b79ea4559 + name: kmer-profiling-hifi-VGP1 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 06564b19b0655c19 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=06564b19b0655c19 + name: Purge-duplicate-contigs-VGP6 (release v0.3.7) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: c556c2270200801d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=c556c2270200801d + name: Purge-duplicate-contigs-VGP6 (release v0.3.8) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 0810be3d7d2b0322 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=0810be3d7d2b0322 + name: Purge-duplicate-contigs-VGP6 (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - __EXTRACT_DATASET__ + - Add_a_column1 + - merqury + - join1 + - gfastats + - tp_cut_tool + - cat1 + - tp_awk_tool + - compose_text_param + - tp_find_and_replace + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 7a97e8ccc332c1e8 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=7a97e8ccc332c1e8 + name: Scaffolding-HiC-VGP8 (release v0.2.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 0aa316f8c6cff444 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=0aa316f8c6cff444 + name: Scaffolding-HiC-VGP8 (release v0.2.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: cac0b8a09d59044b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b + name: Scaffolding-HiC-VGP8 (release v0.2.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 455e68f185fec41b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=455e68f185fec41b + name: Scaffolding-HiC-VGP8 (release v0.2.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 77b2fcf8c805ad5d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=77b2fcf8c805ad5d + name: Scaffolding-HiC-VGP8 (release v0.2.7) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 6ec5728eec9c26d7 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=6ec5728eec9c26d7 + name: Scaffolding with Hi-C data VGP8 (release v0.2.8) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - compose_text_param + - tp_find_and_replace + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 5e3ff382ab802baf + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=5e3ff382ab802baf + name: baredSC_2d_logN (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: d6521e6c247eeaaf + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=d6521e6c247eeaaf + name: baredSC_2d_logN (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 51aaafbd00b91717 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=51aaafbd00b91717 + name: baredSC_2d_logN (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 579da54989f5d55c + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=579da54989f5d55c + name: baredSC_2d_logN (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: 2436bc493e76f438 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2436bc493e76f438 + name: baredSC_2d_logN (release v0.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - baredsc_2d + - baredsc_combine_2d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - 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Lucille Delisle + doi: '' + edam_operation: + - Differential gene expression profiling + - Data retrieval + - Expression correlation analysis + edam_topic: [] + id: d01ff75a4943fa79 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=d01ff75a4943fa79 + name: baredSC_1d_logN (release v0.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - baredsc_combine_1d + - baredsc_1d + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 9804030358c3f844 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=9804030358c3f844 + name: Assembly-Hifi-only-VGP3 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fa37223950a91f34 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=fa37223950a91f34 + name: Assembly-Hifi-only-VGP3 (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - multiqc + - param_value_from_file + - pick_value + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 63789b6f82172679 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=63789b6f82172679 + name: Assembly-Hifi-only-VGP3 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: b5131e3a0ef2676e + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=b5131e3a0ef2676e + name: Assembly-Hifi-only-VGP3 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - __EXTRACT_DATASET__ + - join1 + - tp_find_and_replace + - gfastats + - tp_grep_tool + - cutadapt + - Convert characters1 + - multiqc + - Add_a_column1 + - tp_replace_in_line + - tp_cut_tool + - tp_awk_tool + - param_value_from_file + - pick_value + - hifiasm + - Cut1 + - merqury + - bandage_image + - busco + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Viktoria Isabel Schwarz + - Wolfgang Maier + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Genome indexing + - Read mapping + - Global alignment + - Validation + - Sequence contamination filtering + - Sequence analysis + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 6b1b0a945d367b4c + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=6b1b0a945d367b4c + name: Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - pox + - virology + tools: + - 'EMBOSS: maskseq51' + - split_file_to_collection + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - fasta_compute_length + - collection_element_identifiers + - datamash_ops + - Grep1 + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - samtools_merge + - tp_cat + - tp_sed_tool + - __SORTLIST__ + - qualimap_bamqc + - __APPLY_RULES__ + - param_value_from_file + - bwa_mem + - Cut1 + - __ZIP_COLLECTION__ + - ivar_consensus + - samtools_view + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 8d6d4f848067f3d9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=8d6d4f848067f3d9 + name: RNAseq_PE (release v0.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: b7226d37b25df833 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b7226d37b25df833 + name: RNAseq_PE (release v0.7) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 9b18123afbe1264b + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=9b18123afbe1264b + name: RNAseq_SR (release v0.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Validation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: c2dee690320f9845 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=c2dee690320f9845 + name: RNAseq_SR (release v0.7) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - stringtie + - cutadapt + - tp_awk_tool + - compose_text_param + - rna_star + - multiqc + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6efcacf14bfc18b3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=6efcacf14bfc18b3 + name: ChIPseq_SR (release v0.9) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 14b17f17d03c8424 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=14b17f17d03c8424 + name: ChIPseq_SR (release v0.10) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7a4ee63a04362967 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=7a4ee63a04362967 + name: ChIPseq_PE (release v0.9) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2617fee24459e680 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2617fee24459e680 + name: ChIPseq_PE (release v0.10) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e0b89b4e50d1a99b + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=e0b89b4e50d1a99b + name: CUTandRUN (release v0.10) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2789fb3590727342 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2789fb3590727342 + name: CUTandRUN (release v0.11) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 9d9abc304f3054e3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=9d9abc304f3054e3 + name: Parallel Accession Down (release v0.1.13) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-19' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a53330cff71725b7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=a53330cff71725b7 + name: Parallel Accession Down (release v0.1.14) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-09-19' + versions: 1 +- create_time: '2024-09-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 419e09e4a2fa6d38 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=419e09e4a2fa6d38 + name: 3FT-GRUPO5- 'GUIA-2-Grupo_5-Calidad-con-PycoQC:' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - pycoqc + update_time: '2024-09-05' + versions: 0 +- create_time: '2024-09-05' + creators: [] + doi: '' + edam_operation: + - Box-Whisker plot plotting + - Scatter plot plotting + edam_topic: [] + id: a804d976d351f2fc + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a804d976d351f2fc + name: 2FT-GRUPO5- 'GUIA-2-Calidad-con-Nanoplot' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - nanoplot + update_time: '2024-09-05' + versions: 0 +- create_time: '2024-09-05' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 47cacc06d404a8c6 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=47cacc06d404a8c6 + name: "1FT- 'Grupo_5_GUIA2_Proceso-De-Evaluaci\xF3n_De_Calidad'" + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - multiqc + - fastqe + - cutadapt + update_time: '2024-09-05' + versions: 0 +- create_time: '2024-07-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - De-novo assembly + - Sequence composition calculation + - Cross-assembly + - Mapping assembly + - Sequence assembly visualisation + - Sequencing quality control + edam_topic: [] + id: 479c6b0a96ea1610 + latest_version: 49 + license: GPL-3.0-or-later + link: https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610 + name: Genome assembly workflow for nanopore reads, for TSI + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - genome_assembly + - nanopore + - TSI + tools: + - fastqc + - split_file_to_collection + - collapse_dataset + - flye + - bandage_info + - fasta-stats + - porechop + - bandage_image + - nanofilt + update_time: '2024-09-03' + versions: 49 +- create_time: '2024-08-27' + creators: [] + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: d957bfeb3cd03db0 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d957bfeb3cd03db0 + name: CONTROL DE CALIDAD DEL ENSAMBLAJE DEL GENOMA' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - quast + - merqury + - meryl + - busco + - chromeister + update_time: '2024-09-02' + versions: 1 +- create_time: '2024-09-02' + creators: [] + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - 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Statistical calculation + - Sequencing quality control + edam_topic: [] + id: ed43af416c6a7d3b + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=ed43af416c6a7d3b + name: FT 'Guia 2 nueva parte3' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - pycoqc + update_time: '2024-08-31' + versions: 0 +- create_time: '2024-08-31' + creators: [] + doi: '' + edam_operation: + - Box-Whisker plot plotting + - Scatter plot plotting + edam_topic: [] + id: 8ded019070c6687b + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8ded019070c6687b + name: FT 'Guia 2 nueva parte 2' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - nanoplot + update_time: '2024-08-31' + versions: 0 +- create_time: '2024-08-31' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - 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fastqc + - multiqc + - fastqe + - cutadapt + update_time: '2024-08-31' + versions: 0 +- create_time: '2024-08-31' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: e08b04291839e79a + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e08b04291839e79a + name: 1 FT-GUIA-2-Control-de-Calidad-en-clase + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - multiqc + - fastqe + - cutadapt + update_time: '2024-08-31' + versions: 1 +- create_time: '2024-08-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence composition calculation + - Validation + - Sequence contamination filtering + - Visualisation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 13ce18408ee7acc9 + latest_version: 12 + license: null + link: https://usegalaxy.org.au/published/workflow?id=13ce18408ee7acc9 + name: PCV mapping - paired reads + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - fastp + - pygenomeTracks + - rna_star + - multiqc + update_time: '2024-08-22' + versions: 12 +- create_time: '2024-08-12' + creators: [] + doi: '' + edam_operation: + - Variant calling + - RNA-Seq analysis + - Transcriptome assembly + - Statistical calculation + - Sequence alignment + - Sequence annotation + edam_topic: [] + id: 157e7614ae18849b + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b + name: Gigascience_Indels_SAV_non-normal_demonstration_STS26T-Gent_Workflow (imported + from uploaded file) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - CONVERTER_gz_to_uncompressed + - filter_tabular + - tp_cat + - stringtie + - fasta2tab + - query_tabular + - regexColumn1 + - fasta_merge_files_and_filter_unique_sequences + - bed_to_protein_map + - hisat2 + - gffcompare + - tab2fasta + - gffcompare_to_bed + - 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fastqc + - tp_text_file_with_recurring_lines + - map_param_value + - Cut1 + - Add_a_column1 + - tp_grep_tool + - Convert characters1 + - wc_gnu + - compose_text_param + - param_value_from_file + - pick_value + - cshl_fastq_quality_filter + update_time: '2024-08-12' + versions: 100 +- create_time: '2024-07-03' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: [] + edam_topic: [] + id: f5f9808fb50b6f2c + latest_version: 0 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=f5f9808fb50b6f2c + name: PathoGFAIR (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:microGalaxy + - name:IWC + - name:PathoGFAIR + - name:Nanopore + - name:Collection + tools: [] + update_time: '2024-07-03' + versions: 0 +- create_time: '2024-07-03' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Visualisation + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Mapping + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: eda40b58616a0fe4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4 + name: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - collection_column_join + - collapse_dataset + - __FILTER_FAILED_DATASETS__ + - ggplot2_heatmap + - fasta2tab + - tp_replace_in_column + - tp_sorted_uniq + - clustalw + - Remove beginning1 + - fasta_merge_files_and_filter_unique_sequences + - Grouping1 + - tp_split_on_column + - newick_display + - Count1 + - regexColumn1 + - bedtools_getfastabed + - tp_multijoin_tool + - Cut1 + - fasttree + - tab2fasta + - 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fastqc + - obi_uniq + - seq_filter_by_id + - obi_tab + - Cut1 + - obi_clean + - obi_annotate + - join1 + - obi_stat + - obi_ngsfilter + - ncbi_blastn_wrapper + - obi_grep + - fastq_groomer + - obi_illumina_pairend + - Filter1 + update_time: '2024-06-25' + versions: 0 +- create_time: '2024-06-25' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Variant calling + - Pairwise sequence alignment + edam_topic: [] + id: 244ea5e94237ebad + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad + name: Allele-based Pathogen Identification + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - clair3 + - CONVERTER_gz_to_uncompressed + - table_compute + - snpSift_filter + - Count1 + - Remove beginning1 + - Cut1 + - snpSift_extractFields + - collapse_dataset + - samtools_coverage + - regexColumn1 + - tp_cut_tool + - bcftools_norm + - tp_head_tool + - samtools_depth + - Paste1 + - minimap2 + - bcftools_consensus + update_time: '2024-06-25' + versions: 1 +- create_time: '2024-06-25' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Base-calling + - Genome assembly + - De-novo assembly + - Variant calling + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Sequence assembly + - Sequence assembly visualisation + edam_topic: [] + id: ef8c22c2525063a2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2 + name: Gene-based Pathogen Identification + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:PathoGFAIR + - name:IWC + - name:microGalaxy + tools: + - abricate + - medaka_consensus_pipeline + - collection_element_identifiers + - split_file_to_collection + - flye + - fasta2tab + - bandage_image + - tab2fasta + - compose_text_param + - tp_find_and_replace + - __BUILD_LIST__ + - param_value_from_file + update_time: '2024-06-25' + versions: 1 +- create_time: '2024-06-25' + creators: + - Engy Nasr + - "B\xE9r\xE9nice Batut" + - Paul Zierep + doi: '' + edam_operation: + - Visualisation + - Taxonomic classification + - Aggregation + edam_topic: [] + id: d9ba165e6ae55417 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417 + name: Taxonomy Profiling and Visualization with Krona + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:IWC + tools: + - kraken2 + - krakentools_kreport2krona + - taxonomy_krona_chart + update_time: '2024-06-25' + versions: 1 +- create_time: '2024-06-25' + creators: + - "B\xE9r\xE9nice Batut" + - Engy Nasr + - Paul Zierep + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Taxonomic classification + - Sequence composition calculation + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Visualisation + - Box-Whisker plot plotting + - Sequencing quality control + - Scatter plot plotting + edam_topic: [] + id: 25d52afddaa3451b + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b + name: Nanopore Preprocessing + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:Collection + - name:microGalaxy + - name:PathoGFAIR + - name:Nanopore + - name:IWC + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - krakentools_extract_kraken_reads + - collection_column_join + - Cut1 + - collapse_dataset + - Add_a_column1 + - __FILTER_FAILED_DATASETS__ + - bamtools_split_mapped + - regexColumn1 + - kraken2 + - porechop + - Grep1 + - minimap2 + - multiqc + update_time: '2024-06-25' + versions: 1 +- create_time: '2024-06-11' + creators: [] + doi: '' + edam_operation: + - Data handling + - Sequence alignment + edam_topic: [] + id: 5aff01d0b5fabd84 + latest_version: 5 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5aff01d0b5fabd84 + name: circRNA annotation workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - circRNA + - annotation + tools: + - rna_star + - fastq_dump + - circexplorer + update_time: '2024-06-11' + versions: 5 +- create_time: '2024-05-29' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 84c98a23187d2a36 + latest_version: 0 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=84c98a23187d2a36 + name: Generic variation analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mpxv + - generic + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-05-29' + versions: 0 +- create_time: '2024-05-28' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 39b464084d930a33 + latest_version: 0 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=39b464084d930a33 + name: Variant analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mpxv + - generic + - cloud-costs + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-05-28' + versions: 0 +- create_time: '2024-05-28' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3f39cf407c185724 + latest_version: 0 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=3f39cf407c185724 + name: Variant analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mpxv + - generic + - cloud-costs + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2024-05-28' + versions: 0 +- create_time: '2024-05-28' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Data handling + - Sequence alignment analysis + - Mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 5cd9b9338e75f254 + latest_version: 0 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=5cd9b9338e75f254 + name: RNAseq_PE + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - RNAseq + tools: + - map_param_value + - cufflinks + - bedtools_genomecoveragebed + - bamFilter + - revertR2orientationInBam + - cutadapt + - tp_awk_tool + - compose_text_param + - wig_to_bigWig + - rna_star + - multiqc + - param_value_from_file + update_time: '2024-05-28' + versions: 0 +- create_time: '2024-05-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 69233fb6edfcdde9 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=69233fb6edfcdde9 + name: BINF6000 Assessment 3 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - tp_sort_header_tool + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-05-20' + versions: 1 +- create_time: '2024-05-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 8b8a5b50f2edc72c + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8b8a5b50f2edc72c + name: DE genes of Breast Cancer + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-05-20' + versions: 2 +- create_time: '2024-05-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 4f2818b6620037af + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=4f2818b6620037af + name: Workflow constructed from history 'Group' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - sort1 + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-05-18' + versions: 0 +- create_time: '2024-04-11' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 811bbada546850bd + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=811bbada546850bd + name: C. vibrioides Alignment (SFW) (imported from uploaded file) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - fastp + - trimmomatic + - fastq_dump + - samtools_stats + - featurecounts + - hisat2 + update_time: '2024-05-08' + versions: 1 +- create_time: '2024-05-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: c3e198bc2146b4ad + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c3e198bc2146b4ad + name: Workflow constructed from history 'Breast Cancer Sequencing' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - tp_sort_header_tool + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-05-03' + versions: 0 +- create_time: '2024-04-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: a9fa6101f1fb13e2 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a9fa6101f1fb13e2 + name: workflow for ws1 - s48571959 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-30' + versions: 1 +- create_time: '2024-04-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: d5ecfdbc04b24227 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d5ecfdbc04b24227 + name: Workflow constructed from history 'Workshop 1 Retry' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-30' + versions: 2 +- create_time: '2024-04-29' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 525612313de7591e + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=525612313de7591e + name: Workflow constructed from history 'Copy of 'workshop 1'' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-30' + versions: 0 +- create_time: '2024-04-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: f268c181a47d0cab + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f268c181a47d0cab + name: Workflow constructed from history 'workshop 1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cat1 + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-19' + versions: 0 +- create_time: '2024-04-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 79522a1f7b0c53cb + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=79522a1f7b0c53cb + name: Workflow constructed from history 'workshop 1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cat1 + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-18' + versions: 0 +- create_time: '2024-04-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a8d58b9f85e174c0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=a8d58b9f85e174c0 + name: Parallel Accession Down (release v0.1.12) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-04-18' + versions: 1 +- create_time: '2024-04-16' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d8a4a8bc4fa2f9ee + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d8a4a8bc4fa2f9ee + name: SARS-CoV-2_Assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - ivar_trim + - samtools_sort + - ivar_variants + - jbrowse + - ivar_consensus + - samtools_flagstat + - bwa_mem + update_time: '2024-04-16' + versions: 1 +- create_time: '2023-10-20' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Generation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f52fb12383c8a214 + latest_version: 10 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f52fb12383c8a214 + name: RSV_assembly_workflow_MOHWHOFlu + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - ivar_trim + - samtools_sort + - ivar_variants + - ivar_consensus + - samtools_flagstat + - bwa_mem + update_time: '2024-04-16' + versions: 10 +- create_time: '2024-04-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 2f7c0e3221cbca2f + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2f7c0e3221cbca2f + name: bhoomika shashidhara + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-12' + versions: 1 +- create_time: '2024-04-12' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: f0ced9a5d34b2aff + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f0ced9a5d34b2aff + name: Workflow constructed from history 'workshop1 rajith' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-12' + versions: 0 +- create_time: '2024-04-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: b6db525b1b73394b + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b6db525b1b73394b + name: Workflow constructed from history 'Abinaya workshop 1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-11' + versions: 0 +- create_time: '2024-04-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 97628b0604d5ec77 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=97628b0604d5ec77 + name: lei_bao-47573844 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2024-04-11' + versions: 1 +- create_time: '2024-04-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - 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VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2543e425fa6d5144 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2543e425fa6d5144 + name: ChIPseq_SR (release v0.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 4bd6c5c12fb1a69a + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=4bd6c5c12fb1a69a + name: ChIPseq_PE (release v0.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e57c6d05b560e206 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=e57c6d05b560e206 + name: ChIPseq_PE (release v0.6.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-21' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: d023add11a4f4b09 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=d023add11a4f4b09 + name: Parallel Accession Down (release v0.1.10) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-03-21' + versions: 1 +- create_time: '2024-03-14' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 85e97951bee557f4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=85e97951bee557f4 + name: Parallel Accession Down (release v0.1.10) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2024-03-14' + versions: 1 +- create_time: '2024-03-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Scatter plot plotting + - Box-Whisker plot plotting + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 03b090e75c61c1c3 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=03b090e75c61c1c3 + name: Workflow constructed from history 'Tarea 3' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - nanoplot + update_time: '2024-03-08' + versions: 0 +- create_time: '2024-03-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 31dbe7344d72b903 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=31dbe7344d72b903 + name: Workflow constructed from history 'Tarea 4' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - pycoqc + update_time: '2024-03-08' + versions: 0 +- create_time: '2024-03-07' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 79bf7b0f5e9052d7 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=79bf7b0f5e9052d7 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: c64dcc1e6a67f3e4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=c64dcc1e6a67f3e4 + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 73565f6cb4136370 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=73565f6cb4136370 + name: Scaffolding-BioNano-VGP7 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: ecfb8a08e5a40e15 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=ecfb8a08e5a40e15 + name: Purge-duplicate-contigs-VGP6 (release v0.3.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 6795e545b0cafded + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded + name: 'COVID-19: consensus construction (release v0.4.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 989eb73372135796 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=989eb73372135796 + name: 'COVID-19: variation analysis reporting (release v0.3.3)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-03-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 888eb87b62c4e6dd + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=888eb87b62c4e6dd + name: 'COVID-19: variation analysis on ARTIC PE (release v0.5.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2024-03-07' + versions: 1 +- create_time: '2024-02-22' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 614898119cf0dabf + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=614898119cf0dabf + name: Mitogenome-Assembly-VGP0 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - mitohifi + - compress_file + update_time: '2024-02-22' + versions: 1 +- create_time: '2024-02-22' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 1905ec04d5841f09 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=1905ec04d5841f09 + name: Purge-duplicate-contigs-VGP6 (release v0.3.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-02-22' + versions: 1 +- create_time: '2024-02-15' + creators: + - Anna Syme + doi: '' + edam_operation: + - Visualisation + - Cross-assembly + - Mapping assembly + - Genome assembly + - De-novo assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: d832905fbaf2ca31 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=d832905fbaf2ca31 + name: Genome assembly with Fly (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fasta-stats + - bandage_image + - quast + - flye + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-15' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 4ebf1297793870e7 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=4ebf1297793870e7 + name: Purging-duplicates-one-haplotype-VGP6b (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2024-02-15' + versions: 1 +- create_time: '2024-02-08' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: 3fd10af90a07f771 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=3fd10af90a07f771 + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2024-02-08' + versions: 1 +- create_time: '2024-02-02' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Aggregation + - Pairwise sequence alignment + - Sequence analysis + - Box-Whisker plot plotting + - Mapping assembly + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: d9571b3dfef34e5e + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e + name: " Procedimiento de detecci\xF3n de resistencia a antibi\xF3ticos" + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - nanoplot + - staramr_search + - PlasFlow + - racon + - unicycler + - miniasm + - gfa_to_fa + - minimap2 + - bandage_image + update_time: '2024-02-03' + versions: 0 +- create_time: '2024-01-18' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: b1f45d2f8d8343e9 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=b1f45d2f8d8343e9 + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Peter van Heusden + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Tree-based sequence alignment + - Variant calling + - Sequence contamination filtering + - Methylation analysis + - SNP detection + - Validation + - Variant classification + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7563b3ef697a69fd + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd + name: SARS-CoV-2 Illumina Amplicon pipeline - iVar bas (release v0.2.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - iwc + tools: + - fastp + - ivar_trim + - tp_cat + - pangolin + - nextclade + - tp_sed_tool + - ivar_variants + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - snpeff_sars_cov_2 + - ivar_consensus + - samtools_view + - multiqc + - bwa_mem + update_time: '2024-01-18' + versions: 1 +- create_time: '2024-01-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 41bd0340dcde60ec + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=41bd0340dcde60ec + name: 'COVID-19: variation analysis on WGS SE (release v0.1.4)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2024-01-18' + versions: 1 +- create_time: '2023-12-28' + creators: + - Lucille Delisle + - Mehmet Tekman + - Hans-Rudolf Hotz + - Daniel Blankenberg + - Wendi Bacon + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: 644d8e4c78df8e36 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=644d8e4c78df8e36 + name: scRNA-seq_preprocessing_10X_v3_Bun (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:single-cell + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2023-12-28' + versions: 1 +- create_time: '2023-12-21' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 3d47e0de658b3304 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org.au/published/workflow?id=3d47e0de658b3304 + name: Assembly-decontamination-VGP9 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-12-21' + versions: 1 +- create_time: '2023-12-21' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 5fb44f257e445f56 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org.au/published/workflow?id=5fb44f257e445f56 + name: Assembly-decontamination-VGP9 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-12-21' + versions: 1 +- create_time: '2023-12-18' + creators: [] + doi: '' + edam_operation: + - Fold recognition + - Information extraction + - De-novo assembly + - Query and retrieval + - Sequence motif recognition + - Coding region prediction + - Differential gene expression analysis + - Genome annotation + - Antimicrobial resistance prediction + - Box-Whisker plot plotting + - Sequence clustering + - Filtering + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + - Protein feature detection + - Genome assembly + - Scaffolding + - Homology-based gene prediction + - Transcriptome assembly + - Cross-assembly + - Mapping assembly + - Gene prediction + - Scatter plot plotting + edam_topic: [] + id: 35f39173f0ac9179 + latest_version: 6 + license: null + link: https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179 + name: CSBL-PGAP + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - nanopore + - ONT + - bacterialgenome + - assembly + - annotation + tools: + - nanoplot + - staramr_search + - abricate + - flye + - filtlong + - prokka + - antismash + - eggnog_mapper + - interproscan + - bandage_image + - busco + update_time: '2023-12-20' + versions: 6 +- create_time: '2023-12-14' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: d9c181fd954b629a + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=d9c181fd954b629a + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 08fac3b4c128e597 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=08fac3b4c128e597 + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: d42d7b1aa47e870f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=d42d7b1aa47e870f + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - Add_a_column1 + - merqury + - bandage_image + - gfastats + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: ac8bdc5a0b2d70cd + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=ac8bdc5a0b2d70cd + name: Purge-duplicate-contigs-VGP6 (release v0.3.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 0c11e1ba5e8fa21b + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=0c11e1ba5e8fa21b + name: Purge-duplicate-contigs-VGP6 (release v0.3.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: a1015b83baa0eb6d + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=a1015b83baa0eb6d + name: Purge-duplicate-contigs-VGP6 (release v0.3.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 86eb0ea9dc230f04 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=86eb0ea9dc230f04 + name: Scaffolding-HiC-VGP8 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: ae6a03240680712a + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a + name: Scaffolding-HiC-VGP8 (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-14' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: be35847680078c90 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=be35847680078c90 + name: Scaffolding-HiC-VGP8 (release v0.2.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-12-14' + versions: 1 +- create_time: '2023-12-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 04c9266c6a863fab + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=04c9266c6a863fab + name: Generic variation analysis reporting (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mpvx + - generic + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - compose_text_param + - tp_find_and_replace + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: 0cc8c8875df6bccb + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=0cc8c8875df6bccb + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 6aaaa084d5339c08 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=6aaaa084d5339c08 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: b9d0a39d72b8e5f8 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=b9d0a39d72b8e5f8 + name: kmer-profiling-hifi-VGP1 (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a5ccbb9aced9ac53 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=a5ccbb9aced9ac53 + name: CUTandRUN (release v0.6.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 8b955274ca3ca3dc + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=8b955274ca3ca3dc + name: Generic variation analysis on WGS PE (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mpxv + - generic + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 47672dbb17beeac4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=47672dbb17beeac4 + name: Parallel Accession Down (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 6450b11440eb7fe8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=6450b11440eb7fe8 + name: Parallel Accession Down (release v0.1.9) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 851552cc3e830253 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=851552cc3e830253 + name: 'COVID-19: consensus construction (release v0.4.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: d0d6743450e5060d + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=d0d6743450e5060d + name: 'COVID-19: variation analysis reporting (release v0.3.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-12-07' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ae894cff1d1aba01 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ae894cff1d1aba01 + name: 'COVID-19: variation analysis on WGS PE (release v0.2.4)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2023-12-07' + versions: 1 +- create_time: '2023-11-30' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b20f28151e46d3e0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b20f28151e46d3e0 + name: CUTandRUN (release v0.6.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Anton Nekrutenko + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 25403321a649a92b + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=25403321a649a92b + name: Generic variation analysis on WGS PE (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mpxv + - generic + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 1aca9ce61d2eb5fd + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1aca9ce61d2eb5fd + name: Parallel Accession Down (release v0.1.8) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: feb7258263783c97 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=feb7258263783c97 + name: Parallel Accession Down (release v0.1.9) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: f65b54fcffaa11e5 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5 + name: 'COVID-19: consensus construction (release v0.4.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 800d28ec61b15244 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=800d28ec61b15244 + name: 'COVID-19: variation analysis reporting (release v0.3.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-30' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3c7b55daae7c119b + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=3c7b55daae7c119b + name: 'COVID-19: variation analysis on WGS PE (release v0.2.4)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2023-11-30' + versions: 1 +- create_time: '2023-11-23' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: ab9f7a97baaa7fa6 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=ab9f7a97baaa7fa6 + name: kmer-profiling-hifi-VGP1 (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-23' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: d69016524c11be28 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=d69016524c11be28 + name: Parallel Accession Down (release v0.1.7) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-11-23' + versions: 1 +- create_time: '2023-11-16' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: d2dcd3b54e5082a6 + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org.au/published/workflow?id=d2dcd3b54e5082a6 + name: Assembly-decontamination-VGP9 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-16' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: 11f1564f2bd815d8 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=11f1564f2bd815d8 + name: Scaffolding-BioNano-VGP7 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2023-11-16' + versions: 1 +- create_time: '2023-11-13' + creators: + - Nadolina Brajuka + doi: '' + edam_operation: + - Taxonomic classification + - Data handling + edam_topic: [] + id: 97e55a900db3863b + latest_version: 1 + license: BSD-3-Clause + link: https://usegalaxy.org.au/published/workflow?id=97e55a900db3863b + name: Assembly-decontamination-VGP9 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - tp_cat + - ncbi_dustmasker_wrapper + - gfastats + - tp_sed_tool + - kraken2 + - tp_grep_tool + - tp_find_and_replace + - ncbi_blastn_wrapper + - parse_mito_blast + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: a02c102e179596cb + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=a02c102e179596cb + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: fff2e49bc90e38ca + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=fff2e49bc90e38ca + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Validation + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: f7a866159f1eaecf + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=f7a866159f1eaecf + name: Assembly-Hifi-HiC-phasing-VGP4 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - Add_a_column1 + - tp_replace_in_line + - merqury + - gfastats + - bandage_image + - tp_grep_tool + - tp_sed_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - Paste1 + - multiqc + - param_value_from_file + - busco + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Sequence assembly visualisation + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: e031af90daa2cadf + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=e031af90daa2cadf + name: Assembly-Hifi-Trio-phasing-VGP5 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP + - Reviewed + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - Convert characters1 + - tp_awk_tool + - bandage_image + - param_value_from_file + - busco + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Visualisation + - Data handling + edam_topic: [] + id: bcb0be4f4a0e369f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=bcb0be4f4a0e369f + name: Scaffolding-BioNano-VGP7 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - gfastats + - ggplot2_point + - param_value_from_file + - bionano_scaffold + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: c0aa1f64a89a6115 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=c0aa1f64a89a6115 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 6c5b84bcac127272 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=6c5b84bcac127272 + name: kmer-profiling-hifi-trio-VGP2 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 5364e6ec5b4f48cd + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=5364e6ec5b4f48cd + name: kmer-profiling-hifi-VGP1 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 8dc05e3ba64e981f + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=8dc05e3ba64e981f + name: kmer-profiling-hifi-VGP1 (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: 6c54e7f7a4bf17ed + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=6c54e7f7a4bf17ed + name: kmer-profiling-hifi-VGP1 (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Reviewed + - VGP + tools: + - meryl + - genomescope + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: d83d5ecf31c20490 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=d83d5ecf31c20490 + name: Purge-duplicate-contigs-VGP6 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: fea0e6c02c2f6274 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=fea0e6c02c2f6274 + name: Purge duplicate contigs (WF6 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 40740c32b9a550c9 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=40740c32b9a550c9 + name: Purge duplicate contigs (WF6 (release v0.2.0) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 1ce2a725df3adb74 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=1ce2a725df3adb74 + name: Purge-duplicate-contigs-VGP6 (release v0.3.0) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 7028436ef03171cc + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=7028436ef03171cc + name: Scaffolding-HiC-VGP8 (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Mapping + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 0dbb85f727302a72 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=0dbb85f727302a72 + name: Scaffolding-HiC-VGP8 (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - VGP_curated + tools: + - bwa_mem2 + - __EXTRACT_DATASET__ + - Cut1 + - yahs + - bedtools_bamtobed + - pretext_snapshot + - tp_sort_header_tool + - gfastats + - pretext_map + - ggplot2_point + - bellerophon + - param_value_from_file + - busco + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7c2e7b292803b3e9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=7c2e7b292803b3e9 + name: ChIPseq_SR (release v0.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9bc31dff5bcec42b + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=9bc31dff5bcec42b + name: ChIPseq_PE (release v0.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c87c1f8c4eff415a + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=c87c1f8c4eff415a + name: CUTandRUN (release v0.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-11-13' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 0f7406ada6706c91 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=0f7406ada6706c91 + name: CUTandRUN (release v0.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-11-13' + versions: 1 +- create_time: '2023-06-06' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree analysis + - Visualisation + - Nucleic acid sequence analysis + edam_topic: [] + id: 6b7e565258a9da2a + latest_version: 125 + license: null + link: https://usegalaxy.org.au/published/workflow?id=6b7e565258a9da2a + name: 'analyses-of-shotgun-metagenomics-data-with-metaphlan-v2 ' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - GUCFG2Galaxy + - shotgun + tools: + - metaphlan2krona + - merge_metaphlan_tables + - taxonomy_krona_chart + - Cut1 + - humann2_renorm_table + - humann2 + - metaphlan2 + - humann2_regroup_table + update_time: '2023-10-26' + versions: 125 +- create_time: '2023-10-05' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 97016c7546583e3d + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=97016c7546583e3d + name: Parallel Accession Down (release v0.1.6) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-10-05' + versions: 1 +- create_time: '2023-09-28' + creators: + - Romane Libouban + doi: '' + edam_operation: + - Genome annotation + - Repeat sequence detection + edam_topic: [] + id: ffb1117077f68a9f + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f + name: Repeat masking with RepeatModeler and RepeatMask (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - repeatmasker_wrapper + - repeatmodeler + update_time: '2023-09-28' + versions: 1 +- create_time: '2021-11-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Read mapping + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: cef4a514f35576e5 + latest_version: 13 + license: null + link: https://usegalaxy.org.au/published/workflow?id=cef4a514f35576e5 + name: 'RNAseq Analysis ' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - __FLATTEN__ + - multiqc + - bowtie2 + - featurecounts + - deseq2 + update_time: '2023-09-20' + versions: 13 +- create_time: '2023-09-14' + creators: + - Anna Syme + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Mapping assembly + edam_topic: [] + id: 0c421197e022f323 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=0c421197e022f323 + name: Assembly polishing with long reads (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - minimap2 + - racon + update_time: '2023-09-14' + versions: 1 +- create_time: '2023-09-14' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: e9bf69388d47a0e6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=e9bf69388d47a0e6 + name: Parallel Accession Down (release v0.1.5) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-09-14' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b8968fb0bf796e53 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b8968fb0bf796e53 + name: ChIPseq_SR (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 48a25f8e58d068e6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=48a25f8e58d068e6 + name: ChIPseq_PE (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 2f520cb446adf726 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2f520cb446adf726 + name: CUTandRUN (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-09-07' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 367116498fc5d46b + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=367116498fc5d46b + name: Parallel Accession Down (release v0.1.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2023-09-07' + versions: 1 +- create_time: '2023-08-31' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 1ff259845498b818 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1ff259845498b818 + name: ChIPseq_SR (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-08-31' + versions: 1 +- create_time: '2023-08-31' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 8433a2f79b2e5894 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=8433a2f79b2e5894 + name: ChIPseq_PE (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-08-31' + versions: 1 +- create_time: '2023-07-10' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b0b8b8f79b467cf6 + latest_version: 4 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b0b8b8f79b467cf6 + name: features_overlap + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - tp_cat + - gops_intersect_1 + - Filter1 + update_time: '2023-07-10' + versions: 4 +- create_time: '2023-06-26' + creators: + - Jonathan W. Lawley + - Ido Bar + - Griffith University + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Formatting + - Read summarisation + - RNA-Seq quantification + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 49b5c35b9723fa62 + latest_version: 12 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=49b5c35b9723fa62 + name: Host-Pathogen Dual RNA-Seq DGE + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - combined-genomes + - dual_RNA-Seq + - host-pathogen + - bwa-mem2 + tools: + - bwa_mem2 + - fastp + - picard_AddOrReplaceReadGroups + - cat1 + - qualimap_bamqc + - multiqc + - picard_MarkDuplicates + - featurecounts + update_time: '2023-06-27' + versions: 12 +- create_time: '2023-06-12' + creators: + - "Crist\xF3bal Gallardo Alba" + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Sequence comparison + - Sequence annotation + - Validation + - Sequence contamination filtering + - RNA-Seq analysis + - Transcriptome assembly + - Sequence analysis + - Sequence alignment + - Protein sequence analysis + - Sequencing quality control + edam_topic: [] + id: 6e1e24f9e0326930 + latest_version: 4 + license: CC-BY-SA-4.0 + link: https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930 + name: 'Genome-wide alternative splicing analysis: human version' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - name:alternative-splicing + - name:isoform-switching + tools: + - fastqc + - rseqc_inner_distance + - tp_sorted_uniq + - stringtie_merge + - rseqc_junction_annotation + - rseqc_junction_saturation + - Remove beginning1 + - stringtie + - pfamscan + - tp_grep_tool + - rseqc_infer_experiment + - __FLATTEN__ + - rna_star + - multiqc + - sort1 + - fastp + - gtftobed12 + - tp_cat + - rseqc_geneBody_coverage + - tp_awk_tool + - __FILTER_FROM_FILE__ + - param_value_from_file + - gffread + - Cut1 + - rseqc_read_distribution + - cpat + - isoformswitchanalyzer + update_time: '2023-06-12' + versions: 4 +- create_time: '2023-06-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Taxonomic classification + - Phylogenetic tree generation + - Sequence composition calculation + - Phylogenetic tree visualisation + - Variant calling + - Validation + - Antimicrobial resistance prediction + - Sequencing quality control + edam_topic: [] + id: a61d4bda54de7cd1 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1 + name: M. tuberculosis Variant Analysis tutorial + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - prokaryote + - galaxy-training-network + tools: + - fastqc + - trimmomatic + - snippy + - tbvcfreport + - kraken2 + - jbrowse + - tb_variant_filter + - multiqc + - tb_profiler_profile + update_time: '2023-06-12' + versions: 0 +- create_time: '2023-06-01' + creators: + - Anthony Bretaudeau + - French National Institute for Agriculture, Food, and Environment (INRAE) + doi: '' + edam_operation: + - Operation + - Genome visualisation + - Genome assembly + - Sequence annotation + - Homology-based gene prediction + - Scaffolding + - Genome annotation + - Transcriptome assembly + - Sequence assembly validation + - Gene prediction + - Ab-initio gene prediction + edam_topic: [] + id: 7e40485d1ed45b7c + latest_version: 3 + license: GPL-3.0-or-later + link: https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c + name: 'Genome annotation with Maker, Augustus, Snap, Busco, JBrowse ' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - genome-annotation + tools: + - snap_training + - gffread + - jcvi_gff_stats + - fasta-stats + - maker_map_ids + - augustus_training + - jbrowse + - maker + - busco + update_time: '2023-06-02' + versions: 3 +- create_time: '2023-06-01' + creators: + - Anthony Bretaudeau + doi: '' + edam_operation: + - Fold recognition + - Genome visualisation + - Information extraction + - Genome assembly + - Query and retrieval + - Sequence annotation + - Homology-based gene prediction + - Scaffolding + - Genome annotation + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 4e161a8f5098cc49 + latest_version: 16 + license: GPL-3.0-or-later + link: https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49 + name: Genome annotation with Funannotate, EggNog, Aegean Parseval, Busco, JBrowse + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - genome-annotation + tools: + - funannotate_predict + - eggnog_mapper + - jbrowse + - aegean_parseval + - rna_star + - funannotate_compare + - busco + - funannotate_annotate + update_time: '2023-06-02' + versions: 16 +- create_time: '2023-05-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: 1a107e6611fb9c15 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1a107e6611fb9c15 + name: Workflow constructed from history 'ws1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - rna_starsolo + - cutadapt + - __FLATTEN__ + - htseq_count + - multiqc + update_time: '2023-05-08' + versions: 2 +- create_time: '2023-05-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: af3f40cba4d7afa6 + latest_version: 7 + license: null + link: https://usegalaxy.org.au/published/workflow?id=af3f40cba4d7afa6 + name: Workshop 1 Workflow_47967443 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-05-05' + versions: 7 +- create_time: '2023-05-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e89f0fa8e7f70b9a + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e89f0fa8e7f70b9a + name: Workflow Final + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: [] + update_time: '2023-05-05' + versions: 0 +- create_time: '2023-05-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: e826584d78b69467 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e826584d78b69467 + name: Workflow 'WS1 47541218' DEG Adult vs Embryo dm6 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-05-05' + versions: 0 +- create_time: '2023-05-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e5ac319395fc9f60 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e5ac319395fc9f60 + name: Workflow Final Pupa and Male adult of D. melanogaster + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: [] + update_time: '2023-05-05' + versions: 0 +- create_time: '2023-05-04' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: cef68481b305a516 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=cef68481b305a516 + name: Workflow constructed from history 'WORKSHOP-1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-05-05' + versions: 2 +- create_time: '2023-05-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: d126940d33e63036 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d126940d33e63036 + name: Xiaochun Workflow Workshop1 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - tp_cat + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-05-05' + versions: 0 +- create_time: '2023-04-25' + creators: [] + doi: '' + edam_operation: + - 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cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-05-02' + versions: 0 +- create_time: '2023-05-02' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Read pre-processing + - Primer removal + edam_topic: [] + id: 754149375c3069c4 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=754149375c3069c4 + name: Test workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - cutadapt + update_time: '2023-05-02' + versions: 1 +- create_time: '2023-04-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - Read summarisation + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7ad277dd448e57b3 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7ad277dd448e57b3 + name: Workflow constructed from history 'W-1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - sort1 + - trim_galore + - rna_star + - multiqc + - featurecounts + - deseq2 + - Filter1 + update_time: '2023-05-02' + versions: 0 +- create_time: '2023-03-07' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 5a0fc3b91ae47788 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5a0fc3b91ae47788 + name: Introduction + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2023-05-02' + versions: 0 +- create_time: '2023-05-02' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 978953f492b2b914 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=978953f492b2b914 + name: Workflow constructed from history 'Workshop 1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-05-02' + versions: 0 +- create_time: '2023-04-27' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 14184bc2580a131f + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=14184bc2580a131f + name: Workflow constructed from history 'WS1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - trimmomatic + - multiqc + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-04-29' + versions: 1 +- create_time: '2023-04-26' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: f19d63d7c9a48160 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f19d63d7c9a48160 + name: 'Workflow constructed from history ''WORKSHOP 1- 1 Data Set ' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - trimmomatic + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2023-04-26' + versions: 1 +- create_time: '2023-04-08' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Read mapping + - Primer removal + - Read binning + - Sequence contamination filtering + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 25f65a29ce3c3ee0 + latest_version: 12 + license: null + link: https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0 + name: Cleaning + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - bbtools_bbduk + - trim_galore + - cutadapt + update_time: '2023-04-09' + versions: 12 +- create_time: '2023-03-22' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + - Base-calling + - Genome assembly + - De-novo assembly + - Coding region prediction + - Variant calling + - Genome annotation + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Gene prediction + - Sequence assembly + - Multilocus sequence typing + edam_topic: [] + id: 59618ed15510f531 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=59618ed15510f531 + name: DAMG ONT Genome Assembly (no filt) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - DAMG + - Nanopore + - ONT + - Genome + - Assembly + - Annotation + tools: + - abricate + - medaka_consensus_pipeline + - flye + - mlst + - prokka + - kraken2 + - porechop + update_time: '2023-03-22' + versions: 2 +- create_time: '2022-12-21' + creators: [] + doi: '' + edam_operation: + - Taxonomic classification + - Base-calling + - Genome assembly + - De-novo assembly + - Multilocus sequence typing + - Filtering + - Coding region prediction + - Variant calling + - Genome annotation + - Antimicrobial resistance prediction + - Cross-assembly + - Mapping assembly + - Gene prediction + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: c997a34b55425155 + latest_version: 4 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c997a34b55425155 + name: DAMG ONT Genome Assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - DAMG + - Nanopore + - ONT + - Genome + - Assembly + - Annotation + tools: + - abricate + - medaka_consensus_pipeline + - flye + - filtlong + - prokka + - mlst + - porechop + - kraken2 + update_time: '2023-03-16' + versions: 4 +- create_time: '2023-03-16' + creators: [] + doi: '' + edam_operation: + - Genome annotation + - Taxonomic classification + - Antimicrobial resistance prediction + - Gene prediction + - Coding region prediction + - Multilocus sequence typing + edam_topic: [] + id: e20172eb0f30d6cd + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd + name: DAMG ONT Genome Annotation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - DAMG + - Nanopore + - ONT + - Genome + - Annotation + tools: + - prokka + - kraken2 + - abricate + - mlst + update_time: '2023-03-16' + versions: 1 +- create_time: '2023-02-23' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: a8ec08a1408cd6e7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=a8ec08a1408cd6e7 + name: CUTandRUN (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2023-02-23' + versions: 1 +- create_time: '2023-01-25' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: bc2994ad0fbe07cd + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=bc2994ad0fbe07cd + name: "Copy of Workflow constructed from history 'An\xE1lisis Exoma'" + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + update_time: '2023-01-25' + versions: 0 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7d268e7209a68e2e + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=7d268e7209a68e2e + name: ChIPseq_SR (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 32d28f800adcea42 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=32d28f800adcea42 + name: ATACseq (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 52056336f24eccf6 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=52056336f24eccf6 + name: ATACseq (release v0.4) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2023-01-19' + versions: 1 +- create_time: '2023-01-19' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: b191da6e594747fb + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b191da6e594747fb + name: ChIPseq_PE (release v0.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2023-01-19' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: e92b4d8dfa2f1cf7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=e92b4d8dfa2f1cf7 + name: ChIPseq_SR (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 3e7fcfd23872ad0d + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=3e7fcfd23872ad0d + name: ATACseq (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 7ad9410e36ee9ea1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=7ad9410e36ee9ea1 + name: ChIPseq_PE (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-12-01' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 57b558e1a76c09e1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=57b558e1a76c09e1 + name: CUTandRUN (release v0.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - CUTnRUN + tools: + - bedtools_bamtobed + - tp_grep_tool + - cutadapt + - wig_to_bigWig + - macs2_callpeak + - multiqc + - picard_MarkDuplicates + - bowtie2 + - samtool_filter2 + update_time: '2022-12-01' + versions: 1 +- create_time: '2022-11-10' + creators: [] + doi: '' + edam_operation: + - Gene prediction + - Genome annotation + - Genome visualisation + - Coding region prediction + edam_topic: [] + id: 6c67e22d18566af3 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=6c67e22d18566af3 + name: Workflow constructed from history 'gene annotation' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - prokka + - jbrowse + update_time: '2022-11-10' + versions: 1 +- create_time: '2022-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Transcriptome assembly + - Data handling + - Genome assembly + - Sequence assembly validation + - Mapping + - Sequence alignment + - Scaffolding + edam_topic: [] + id: 29f0c07c8a24b542 + latest_version: 5 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542 + name: VGP HiC (Yahs) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgp + - assembly + - hi-c + - yahs + tools: + - bwa_mem2 + - sort1 + - __EXTRACT_DATASET__ + - bedtools_bamtobed + - samtools_sort + - pretext_snapshot + - yahs + - gfastats + - pretext_map + - gfa_to_fa + - bellerophon + - param_value_from_file + - busco + update_time: '2022-11-10' + versions: 5 +- create_time: '2022-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: + - Data handling + - Genome assembly + - De-novo assembly + - Mapping + - Scaffolding + - Transcriptome assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: e07866576cc2f467 + latest_version: 5 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467 + name: VGP HiC + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgp + - assembly + - hi-c + - salsa + tools: + - bwa_mem2 + - sort1 + - __EXTRACT_DATASET__ + - bedtools_bamtobed + - samtools_sort + - pretext_snapshot + - gfastats + - pretext_map + - gfa_to_fa + - tp_find_and_replace + - bellerophon + - param_value_from_file + - salsa + - busco + update_time: '2022-11-10' + versions: 5 +- create_time: '2022-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 7909da83448d8bf4 + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=7909da83448d8bf4 + name: Purgedups + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgp + - assembly + - hifi + - purge_dups + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2022-11-10' + versions: 2 +- create_time: '2022-11-09' + creators: + - Galaxy + - VGP + - Delphine Lariviere + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: 98d3def7da131b4c + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=98d3def7da131b4c + name: Long read assembly with Hifiasm and HiC data + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgp + - assembly + - hi-c + - hifiasm + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - gfa_to_fa + - Convert characters1 + - tp_awk_tool + - param_value_from_file + - busco + update_time: '2022-11-10' + versions: 2 +- create_time: '2022-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 53cbacc71790c41b + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=53cbacc71790c41b + name: VGP Bionano + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgp + - assembly + - bionano + tools: + - param_value_from_file + - bionano_scaffold + - gfastats + update_time: '2022-11-10' + versions: 2 +- create_time: '2022-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + edam_topic: [] + id: 094655df3ccd0b00 + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=094655df3ccd0b00 + name: Purgedups- custom cutoffs for alternate assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgs + - assembly + - hifi + - purge_dups + tools: + - merqury + - gfastats + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - purge_dups + update_time: '2022-11-10' + versions: 1 +- create_time: '2022-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Scaffolding + - Read binning + - Pairwise sequence alignment + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: 1dcc1b25c9091fbf + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=1dcc1b25c9091fbf + name: Purgedups- custom cutoffs for primary assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgp + - assembly + - hifi + - purge_dups + tools: + - Cut1 + - Add_a_column1 + - merqury + - gfastats + - cat1 + - tp_easyjoin_tool + - tp_awk_tool + - minimap2 + - param_value_from_file + - busco + - purge_dups + update_time: '2022-11-10' + versions: 1 +- create_time: '2022-11-09' + creators: + - Galaxy + - VGP + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Data handling + - Genome assembly + - De-novo assembly + - Primer removal + - Scaffolding + - Sequence trimming + - Transcriptome assembly + - Read pre-processing + - Sequence assembly validation + edam_topic: [] + id: afab89bc468da8b3 + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=afab89bc468da8b3 + name: Long read assembly with Hifiasm + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgp + - assembly + - hifi + - hifiasm + tools: + - hifiasm + - Cut1 + - tp_replace_in_line + - merqury + - gfastats + - tp_grep_tool + - tp_easyjoin_tool + - cutadapt + - gfa_to_fa + - Convert characters1 + - tp_awk_tool + - param_value_from_file + - busco + update_time: '2022-11-10' + versions: 2 +- create_time: '2022-11-09' + creators: + - VGP + - Galaxy + doi: '' + edam_operation: [] + edam_topic: [] + id: d9ee934bbae0fa01 + latest_version: 2 + license: CC-BY-4.0 + link: https://usegalaxy.org.au/published/workflow?id=d9ee934bbae0fa01 + name: Meryl Database Creation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - vgp + - assembly + - hifi + - meryl + - genome_profiling + tools: + - meryl + - genomescope + update_time: '2022-11-10' + versions: 2 +- create_time: '2022-10-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 9787c8b7adeedb0c + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=9787c8b7adeedb0c + name: ChIPseq_SR (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ChIP + tools: + - tp_grep_tool + - cutadapt + - macs2_callpeak + - multiqc + - wig_to_bigWig + - bowtie2 + - samtool_filter2 + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-27' + creators: + - Lucille Delisle + doi: '' + edam_operation: + - Formatting + - Data handling + - Sequence alignment analysis + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Validation + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 6b3df543536faf8c + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=6b3df543536faf8c + name: ATACseq (release v0.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ATACseq + tools: + - bedtools_coveragebed + - bedtools_mergebed + - samtools_idxstats + - bedtools_bamtobed + - bamFilter + - tp_grep_tool + - cat1 + - cutadapt + - tp_awk_tool + - bedtools_slopbed + - wig_to_bigWig + - macs2_callpeak + - samtools_view + - picard_MarkDuplicates + - multiqc + - bowtie2 + - pe_histogram + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-27' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 2b71eb1dc2aa28a1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1 + name: 'COVID-19: consensus construction (release v0.4)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-10-27' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 1764bb1f506212e8 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1764bb1f506212e8 + name: 'COVID-19: variation analysis reporting (release v0.3)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-10-27' + versions: 1 +- create_time: '2022-05-03' + creators: + - Gareth Price + doi: '' + edam_operation: + - Phasing + - k-mer counting + - Genome assembly + - De-novo assembly + - Scaffolding + - Visualisation + - Transcriptome assembly + - Sequence assembly validation + edam_topic: [] + id: df11f09771e73e04 + latest_version: 7 + license: GPL-3.0-or-later + link: https://usegalaxy.org.au/published/workflow?id=df11f09771e73e04 + name: Genome assessment post assembly v1.0 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - hifi + - hifiasm + - QC + - Quast + - Meryl + - Merqury + - BUSCO + tools: + - quast + - merqury + - fasta-stats + - meryl + - busco + update_time: '2022-10-17' + versions: 7 +- create_time: '2022-09-01' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 954318db8c8d9219 + latest_version: 19 + license: null + link: https://usegalaxy.org.au/published/workflow?id=954318db8c8d9219 + name: PreProcSEQ + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - RNA-Seq + - transcription + - matrix + - counts + tools: + - fastqc + - multiqc + - trimmomatic + - salmon + update_time: '2022-10-11' + versions: 19 +- create_time: '2022-09-27' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + edam_topic: [] + id: 13a2c5bd07705985 + latest_version: 14 + license: null + link: https://usegalaxy.org.au/published/workflow?id=13a2c5bd07705985 + name: Whole-retina differential gene expression + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - Filter1 + - tab2fasta + - deseq2 + - salmon + update_time: '2022-09-29' + versions: 14 +- create_time: '2021-07-15' + creators: + - Gareth Price + doi: '' + edam_operation: + - Sequence assembly visualisation + edam_topic: [] + id: 36604d0ab0dee988 + latest_version: 32 + license: GPL-3.0-or-later + link: https://usegalaxy.org.au/published/workflow?id=36604d0ab0dee988 + name: PacBio HiFi genome assembly using hifiasm v2.0 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - fastq + - hifiasm + - HiFi + - genome_assembly + tools: + - hifiasm + - bandage_info + - hifiadapterfilt + - fasta-stats + - gfa_to_fa + - bandage_image + update_time: '2022-09-19' + versions: 32 +- create_time: '2022-08-18' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: b5e546197f47f3ec + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b5e546197f47f3ec + name: exploring iris dataset with stats and plots + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - Remove beginning1 + - csv_to_tabular + - datamash_ops + - tp_cut_tool + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2022-08-18' + versions: 2 +- create_time: '2022-08-04' + creators: [] + doi: '' + edam_operation: + - De-novo assembly + - Read mapping + - Primer removal + - Pairwise sequence alignment + - Sequence assembly validation + - Phasing + - k-mer counting + - Genome assembly + - Genome indexing + - Mapping + - Scaffolding + - Read binning + - Sequence trimming + - Visualisation + - Transcriptome assembly + - Generation + - Read pre-processing + - Sequence alignment + edam_topic: [] + id: 434127690544d0e9 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=434127690544d0e9 + name: 'VGP assembly: training workflow (imported from GTN materials August 4 2022)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + tools: + - genomescope + - collapse_dataset + - pretext_snapshot + - gfa_to_fa + - tp_find_and_replace + - bellerophon + - bedtools_bamtobed + - tp_grep_tool + - cat1 + - cutadapt + - Convert characters1 + - sort1 + - Add_a_column1 + - tp_cut_tool + - minimap2 + - meryl + - param_value_from_file + - salsa + - purge_dups + - bwa_mem + - hifiasm + - quast + - merqury + - pretext_map + - bionano_scaffold + - busco + update_time: '2022-08-04' + versions: 1 +- create_time: '2020-06-21' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Sequence assembly visualisation + - Sequencing quality control + edam_topic: [] + id: 813a4938397cf6ee + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=813a4938397cf6ee + name: Generic Assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Assembly + - Bacterial + tools: + - fastqc + - bandage_image + - fastp + - spades + update_time: '2022-07-18' + versions: 3 +- create_time: '2022-06-28' + creators: [] + doi: '' + edam_operation: + - Mapping + - Sequencing quality control + edam_topic: [] + id: 5cf5334877cc1297 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5cf5334877cc1297 + name: GA-virReport-Stats (Public) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Ga-virReport-confidence + tools: + - bcftools_call + - bowtie_wrapper + - bedtools_genomecoveragebed + - bedtools_maskfastabed + - qualimap_bamqc + - tp_awk_tool + - sam_to_bam + - ncbi_blastn_wrapper + - ncbi_blastdbcmd_wrapper + - bcftools_mpileup + - bcftools_consensus + update_time: '2022-06-28' + versions: 1 +- create_time: '2022-06-28' + creators: + - Ruvini Lelwala + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence alignment analysis + - De-novo assembly + - Local alignment + - Sequence composition calculation + - Global alignment + - Primer removal + - Sequence contamination filtering + - Sequence trimming + - Sequence analysis + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: dccc8fb49d61ac33 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33 + name: GA-VirReport-Single_input_files (Public) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - GA-virReport + tools: + - fastqc + - fastp + - velvetg + - cap3 + - bowtie_wrapper + - umi_tools_extract + - cutadapt + - ncbi_tblastn_wrapper + - ncbi_blastn_wrapper + - ncbi_makeblastdb + - 'EMBOSS: getorf42' + - velveth + update_time: '2022-06-28' + versions: 1 +- create_time: '2022-06-28' + creators: + - Ruvini Lelwala + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Sequence alignment analysis + - De-novo assembly + - Local alignment + - Sequence composition calculation + - Global alignment + - Primer removal + - Sequence contamination filtering + - Sequence trimming + - Sequence analysis + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 94c7fdcbbc7b428a + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a + name: GA-VirReport-Multiple_input_files_(Public) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - GA-virReport + tools: + - fastqc + - fastp + - velvetg + - cap3 + - bowtie_wrapper + - umi_tools_extract + - cat_multiple + - cutadapt + - ncbi_tblastn_wrapper + - ncbi_blastn_wrapper + - ncbi_makeblastdb + - 'EMBOSS: getorf42' + - velveth + update_time: '2022-06-28' + versions: 2 +- create_time: '2022-06-06' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: a77ce877e786d44a + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a + name: Generic consensus construction from VCF calls + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mlxv + - generic + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-06-06' + versions: 1 +- create_time: '2022-06-06' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: b9e82e3fae56d8b4 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b9e82e3fae56d8b4 + name: Genetic variation analysis reporting + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mpvx + - generic + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - compose_text_param + - tp_find_and_replace + - Filter1 + update_time: '2022-06-06' + versions: 1 +- create_time: '2022-06-06' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 06ba34da322f46f1 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=06ba34da322f46f1 + name: Generic variation analysis on WGS PE data + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - mpxv + - generic + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - snpEff_build_gb + - samtools_stats + - lofreq_filter + - snpEff + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-06-06' + versions: 1 +- create_time: '2022-06-01' + creators: [] + doi: '' + edam_operation: + - Genome annotation + - Visualisation + - Coding region prediction + - Genome assembly + - Gene prediction + - Aggregation + - Sequence assembly validation + edam_topic: [] + id: 8f7d5ebead46a6d0 + latest_version: 8 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0 + name: Di Marzio Workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - quast + - trimmomatic + - spades + - unicycler + - prokka + update_time: '2022-06-04' + versions: 8 +- create_time: '2022-04-05' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1e71b5232b9b4d2a + latest_version: 8 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1e71b5232b9b4d2a + name: Stacks RAD-seq de novo workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - stacks2_ustacks + - stacks2_cstacks + - stacks2_populations + - stacks2_gstacks + - stacks2_sstacks + - stacks2_tsv2bam + update_time: '2022-05-31' + versions: 8 +- create_time: '2022-05-16' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: f7adc76331620f34 + latest_version: 23 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f7adc76331620f34 + name: Stacks RAD-seq reference-guided workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - bwa_mem2 + - stacks2_populations + - samtools_stats + - stacks2_gstacks + - samtools_view + - multiqc + update_time: '2022-05-31' + versions: 23 +- create_time: '2022-05-18' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 44bad90b676d58f6 + latest_version: 7 + license: null + link: https://usegalaxy.org.au/published/workflow?id=44bad90b676d58f6 + name: Partial ref-guided workflow - bwa mem only + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - bwa_mem2 + - samtools_view + - samtools_stats + - multiqc + update_time: '2022-05-19' + versions: 7 +- create_time: '2022-05-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a401ad5349b44dfb + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a401ad5349b44dfb + name: Partial ref-guided workflow - gstacks and pops + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - stacks2_populations + - stacks2_gstacks + update_time: '2022-05-18' + versions: 2 +- create_time: '2022-05-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: ca45322bff44e73a + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=ca45322bff44e73a + name: 'Partial de novo workflow: c-s-g-pops only' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - stacks2_cstacks + - stacks2_populations + - stacks2_gstacks + - stacks2_sstacks + - stacks2_tsv2bam + update_time: '2022-05-18' + versions: 2 +- create_time: '2022-05-18' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9b3f3d331d0b2892 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=9b3f3d331d0b2892 + name: 'Partial de novo workflow: ustacks only' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - stacks2_ustacks + update_time: '2022-05-18' + versions: 1 +- create_time: '2022-05-17' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 7b203d52f496e2c7 + latest_version: 29 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7b203d52f496e2c7 + name: QC of RADseq reads + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - multiqc + - fastp + - cutadapt + update_time: '2022-05-18' + versions: 29 +- create_time: '2022-05-18' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - Read summarisation + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 67191ea9fe977e08 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=67191ea9fe977e08 + name: Workflow constructed from history 'BINF6000 Workshop 1 (user stream) RNAseq + Analysis' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - hisat2 + - multiqc + - featurecounts + - deseq2 + - Filter1 + update_time: '2022-05-18' + versions: 1 +- create_time: '2022-05-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: b452e983e08b9298 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b452e983e08b9298 + name: Workflow constructed from history 'embryo and pupa' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2022-05-14' + versions: 0 +- create_time: '2022-05-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: f5c0b0bc5e023e42 + latest_version: 4 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f5c0b0bc5e023e42 + name: Workflow constructed from history '6000Yi' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2022-05-12' + versions: 4 +- create_time: '2022-05-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 975ddb0eb436f1fd + latest_version: 5 + license: null + link: https://usegalaxy.org.au/published/workflow?id=975ddb0eb436f1fd + name: Workflow constructed from history '9_dataset' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - 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Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: fb644a9649f36f40 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=fb644a9649f36f40 + name: Workshop 1 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - sort1 + - cutadapt + - gff_filter_by_attribute + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2022-05-12' + versions: 2 +- create_time: '2022-05-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Validation + - Differential gene expression analysis + - RNA-Seq analysis + - Read summarisation + - 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fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2022-05-12' + versions: 0 +- create_time: '2022-05-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: afd9a8bbc07f9c3f + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=afd9a8bbc07f9c3f + name: BINF 6000 WS1 ZW + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2022-05-11' + versions: 0 +- create_time: '2022-05-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 374311292d72c9f9 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=374311292d72c9f9 + name: Workflow constructed from history 'workshop' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2022-05-11' + versions: 0 +- create_time: '2022-05-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - RNA-Seq analysis + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 3c727d5cd349a846 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=3c727d5cd349a846 + name: User12 Embryo and Pupa + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - cutadapt + - multiqc + - Filter1 + - featurecounts + - deseq2 + - hisat2 + update_time: '2022-05-11' + versions: 0 +- create_time: '2022-03-15' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: acaca80c4a0c76c8 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=acaca80c4a0c76c8 + name: 'QC AND FILTERING ' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2022-05-11' + versions: 2 +- create_time: '2022-04-30' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Differential gene expression analysis + - Sequence trimming + - Read summarisation + - RNA-Seq analysis + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ae773dfaa074cb72 + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=ae773dfaa074cb72 + name: ' BINF6000_Workshop1_workflow' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - deg_annotate + - Cut1 + - join1 + - ggplot2_heatmap2 + - cat1 + - cutadapt + - rna_star + - multiqc + - featurecounts + - deseq2 + - Filter1 + update_time: '2022-05-03' + versions: 3 +- create_time: '2021-09-08' + creators: + - Gareth Price + doi: '' + edam_operation: + - Pairwise sequence alignment + - Read binning + - Scaffolding + - Genome assembly + edam_topic: [] + id: e5dfeff4a3068f36 + latest_version: 7 + license: GPL-3.0-or-later + link: https://usegalaxy.org.au/published/workflow?id=e5dfeff4a3068f36 + name: Purge duplicates from hifiasm assembly v1.0 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Assembly + - purge_dups + - HiFi + tools: + - minimap2 + - fasta-stats + - purge_dups + update_time: '2022-03-25' + versions: 7 +- create_time: '2021-09-08' + creators: + - Gareth Price + doi: '' + edam_operation: + - Sequence composition calculation + - Formatting + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: db322fe56af3ee5b + latest_version: 8 + license: GPL-3.0-or-later + link: https://usegalaxy.org.au/published/workflow?id=db322fe56af3ee5b + name: BAM to FASTQ + QC v1.0 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - BAM + - FastQ + - Conversion + - QC + tools: + - picard_SamToFastq + - fastqc + - samtools_flagstat + update_time: '2022-03-25' + versions: 8 +- create_time: '2021-09-21' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c6bc6ee668ab51ab + latest_version: 22 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c6bc6ee668ab51ab + name: scRNAseq with AnnData + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - scRNAseq + - single-cell + - transcriptomics + tools: + - tp_cat + update_time: '2022-03-23' + versions: 22 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: b920b02a23f94d11 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=b920b02a23f94d11 + name: 'COVID-19: variation analysis reporting (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 7cc2b5010c56f117 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=7cc2b5010c56f117 + name: 'COVID-19: variation analysis reporting (release v0.1.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 5a975438c8752269 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=5a975438c8752269 + name: 'COVID-19: variation analysis reporting (release v0.1.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: 1782d699b0166725 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1782d699b0166725 + name: 'COVID-19: variation analysis reporting (release v0.1.3)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: [] + edam_topic: [] + id: fbc732db2a2821b0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=fbc732db2a2821b0 + name: 'COVID-19: variation analysis reporting (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 1cf77dc01e5f25d3 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1cf77dc01e5f25d3 + name: Parallel Accession Down (release v0.1.1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: a1ccfa620265e45c + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=a1ccfa620265e45c + name: Parallel Accession Down (release v0.1.2) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Marius van den Beek + - IWC + doi: '' + edam_operation: + - Data handling + edam_topic: [] + id: 7c3b103c8ec8aecf + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=7c3b103c8ec8aecf + name: Parallel Accession Down (release v0.1.3) + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - param_value_from_file + - fasterq_dump + - split_file_to_collection + - __APPLY_RULES__ + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 1dd4392c51766383 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=1dd4392c51766383 + name: 'COVID-19: variation analysis on WGS SE (release v0.1.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: fe4e34a407157389 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=fe4e34a407157389 + name: 'COVID-19: variation analysis on WGS SE (release v0.1.3)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 27205feb28b0ce06 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=27205feb28b0ce06 + name: 'COVID-19: variation analysis on WGS PE (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ca7fc6e2adbf1f26 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ca7fc6e2adbf1f26 + name: 'COVID-19: variation analysis on WGS PE (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: d3521c05077192df + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=d3521c05077192df + name: 'COVID-19: variation analysis on WGS PE (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ba30cc4a84c449f9 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ba30cc4a84c449f9 + name: 'COVID-19: variation analysis on WGS PE (release v0.2.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + - iwc + - emergen_validated + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: be9213411c520096 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=be9213411c520096 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 094a545d44ce28cc + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=094a545d44ce28cc + name: 'COVID-19: variation analysis on ARTIC PE (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: c1ce3f2ae7c81c3e + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=c1ce3f2ae7c81c3e + name: 'COVID-19: variation analysis on ARTIC PE (release v0.3)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3223ceaa2b58d940 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=3223ceaa2b58d940 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3c657dd766d02f6a + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=3c657dd766d02f6a + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 810242a3dc4f6170 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=810242a3dc4f6170 + name: 'COVID-19: variation analysis on ARTIC PE (release v0.4.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - lofreq_filter + - __FLATTEN__ + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Validation + - SNP detection + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2b2ce7e1206d177d + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2b2ce7e1206d177d + name: 'COVID-19: variation analysis on ARTIC PE (release v0.5)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - snpSift_filter + - vcfvcfintersect + - __FILTER_FAILED_DATASETS__ + - samtools_stats + - snpeff_sars_cov_2 + - ivar_removereads + - lofreq_filter + - __FLATTEN__ + - compose_text_param + - multiqc + - fastp + - ivar_trim + - tp_replace_in_line + - qualimap_bamqc + - bcftools_annotate + - bwa_mem + - lofreq_call + - lofreq_indelqual + - samtools_view + - lofreq_viterbi + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - Pairwise sequence alignment + - SNP detection + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 4bc8ac41ecff7daf + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=4bc8ac41ecff7daf + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - lofreq_filter + - tp_find_and_replace + - minimap2 + - samtools_view + - snpeff_sars_cov_2 + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - SNP detection + - Pairwise sequence alignment + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 48a60965b6b3ff54 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=48a60965b6b3ff54 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - snpeff_sars_cov_2 + - lofreq_filter + - minimap2 + - samtools_view + - tp_find_and_replace + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - SNP detection + - Pairwise sequence alignment + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 888f8377eb6eabf2 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=888f8377eb6eabf2 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - snpeff_sars_cov_2 + - lofreq_filter + - minimap2 + - samtools_view + - tp_find_and_replace + - multiqc + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: ba7a9d4c857d26b7 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ba7a9d4c857d26b7 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.3)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Mapping + - Variant calling + - SNP detection + - Validation + - Sequence contamination filtering + - Pairwise sequence alignment + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 932bad88f8dc8d33 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=932bad88f8dc8d33 + name: 'COVID-19: variation analysis of ARTIC ONT (release v0.3.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - __FILTER_FAILED_DATASETS__ + - tp_replace_in_column + - samtools_stats + - snpeff_sars_cov_2 + - tp_find_and_replace + - medaka_variant + - datamash_ops + - lofreq_filter + - __FLATTEN__ + - multiqc + - fastp + - medaka_consensus + - ivar_trim + - Add_a_column1 + - qualimap_bamqc + - minimap2 + - param_value_from_file + - bcftools_annotate + - bedtools_intersectbed + - bamleftalign + - samtools_view + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: ebd1ee73906fdea0 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0 + name: 'COVID-19: consensus construction (release v0.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 5cd7f1824db7a960 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960 + name: 'COVID-19: consensus construction (release v0.2.1)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 2955ea7be1cdda29 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29 + name: 'COVID-19: consensus construction (release v0.2.2)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-18' + creators: + - Wolfgang Maier + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 4b681937a01df465 + latest_version: 1 + license: MIT + link: https://usegalaxy.org.au/published/workflow?id=4b681937a01df465 + name: 'COVID-19: consensus construction (release v0.3)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - snpSift_extractFields + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - compose_text_param + - bcftools_consensus + - Filter1 + update_time: '2022-03-18' + versions: 1 +- create_time: '2022-03-16' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: eda00feabdd21711 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=eda00feabdd21711 + name: Workflow constructed from history 'Find SNP in Exons of human X chromosome' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - sort1 + - datamash_ops + - bedtools_intersectbed + - comp1 + - Show beginning1 + update_time: '2022-03-16' + versions: 0 +- create_time: '2022-02-08' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: 0f71c97671bb401f + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=0f71c97671bb401f + name: Workflow ORFs and CDSs + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - ncbi_acc_download + - get_orfs_or_cdss + - jbrowse + - collapse_dataset + update_time: '2022-03-11' + versions: 2 +- create_time: '2022-03-10' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: bf999071343171b7 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=bf999071343171b7 + name: Find exons with the highest number of features + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - sort1 + - datamash_ops + - join1 + - bedtools_intersectbed + - Show beginning1 + update_time: '2022-03-10' + versions: 1 +- create_time: '2022-03-09' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: cb6f49d4ebfa0891 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=cb6f49d4ebfa0891 + name: 'Workshop 2: Exploring CDSs and ORFs using SARS-CoV-2' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - ncbi_acc_download + - get_orfs_or_cdss + - jbrowse + - collapse_dataset + update_time: '2022-03-09' + versions: 1 +- create_time: '2022-03-02' + creators: [] + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Read mapping + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Sequence file editing + - Sequencing quality control + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: 9c60b83feaa22415 + latest_version: 12 + license: null + link: https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415 + name: SARS-CoV-2 genome assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - GTN + - assembly + tools: + - samtools_fastx + - fasta_filter_by_length + - nanoplot + - fastp + - samtools_view + - bandage_info + - collapse_dataset + - unicycler + - __ZIP_COLLECTION__ + - bandage_image + - samtools_stats + - minimap2 + - multiqc + - bowtie2 + - seqtk_sample + update_time: '2022-03-06' + versions: 12 +- create_time: '2022-02-22' + creators: [] + doi: '' + edam_operation: + - Sequence contamination filtering + - Sequencing quality control + edam_topic: [] + id: 77951619443e6f87 + latest_version: 5 + license: null + link: https://usegalaxy.org.au/published/workflow?id=77951619443e6f87 + name: fastp workflow - testing only + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - galaxy-australia-workflows + - qc + - statistics + tools: + - fastp + update_time: '2022-03-04' + versions: 5 +- create_time: '2021-06-15' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Sequence file editing + - Data handling + edam_topic: [] + id: 324c683a8e2fa5b0 + latest_version: 29 + license: null + link: https://usegalaxy.org.au/published/workflow?id=324c683a8e2fa5b0 + name: Prepare test data - remove chloroplast reads and subsample to 10% + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - seqtk_seq + - samtools_fastx + - minimap2 + update_time: '2021-11-09' + versions: 29 +- create_time: '2021-09-15' + creators: + - Anna Syme + doi: '' + edam_operation: + - Sequence contamination filtering + - Sequencing quality control + edam_topic: [] + id: c5f000229dd93599 + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c5f000229dd93599 + name: Trim and filter reads - fastp + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - fastp + update_time: '2021-11-09' + versions: 3 +- create_time: '2021-05-26' + creators: + - Anna Syme + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Scatter plot plotting + - Box-Whisker plot plotting + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 3ac73a2f00423326 + latest_version: 19 + license: null + link: https://usegalaxy.org.au/published/workflow?id=3ac73a2f00423326 + name: Data QC + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - fastqc + - multiqc + - nanoplot + update_time: '2021-11-09' + versions: 19 +- create_time: '2021-08-03' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Mapping assembly + edam_topic: [] + id: 1ff6aabb7e3954ac + latest_version: 16 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1ff6aabb7e3954ac + name: Racon polish with Illumina reads (R1 only), x2 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - minimap2 + - racon + update_time: '2021-11-09' + versions: 16 +- create_time: '2021-07-27' + creators: + - Anna Syme + doi: '' + edam_operation: + - Pairwise sequence alignment + - Genome assembly + - Mapping assembly + edam_topic: [] + id: 45e9910f46a210d8 + latest_version: 18 + license: null + link: https://usegalaxy.org.au/published/workflow?id=45e9910f46a210d8 + name: Racon polish with long reads, x4 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - minimap2 + - racon + update_time: '2021-11-09' + versions: 18 +- create_time: '2021-08-03' + creators: + - Anna Syme + doi: '' + edam_operation: + - Variant calling + - Sequence assembly + - Base-calling + edam_topic: [] + id: 705658f68ae73930 + latest_version: 51 + license: null + link: https://usegalaxy.org.au/published/workflow?id=705658f68ae73930 + name: Assembly polishing + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - fasta-stats + - medaka_consensus_pipeline + update_time: '2021-11-09' + versions: 51 +- create_time: '2021-09-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: d7c2d0d49b1a6c86 + latest_version: 4 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d7c2d0d49b1a6c86 + name: kmer counting - meryl + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - meryl + - genomescope + update_time: '2021-11-09' + versions: 4 +- create_time: '2021-07-27' + creators: + - Anna Syme + doi: '' + edam_operation: + - Scaffolding + - Visualisation + - Transcriptome assembly + - Genome assembly + - Sequence assembly validation + edam_topic: [] + id: 243c67fa4312855e + latest_version: 21 + license: null + link: https://usegalaxy.org.au/published/workflow?id=243c67fa4312855e + name: Assess genome quality + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - quast + - busco + update_time: '2021-11-09' + versions: 21 +- create_time: '2021-05-26' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Cross-assembly + - Mapping assembly + - Genome assembly + - De-novo assembly + - Sequence assembly visualisation + - Sequence assembly validation + edam_topic: [] + id: 5b32e2f0d390a4ba + latest_version: 33 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5b32e2f0d390a4ba + name: Assembly with Flye + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: + - quast + - flye + - barchart_gnuplot + - fasta-stats + - bandage_image + update_time: '2021-11-09' + versions: 33 +- create_time: '2021-07-26' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 983aa4c8630255bc + latest_version: 111 + license: null + link: https://usegalaxy.org.au/published/workflow?id=983aa4c8630255bc + name: Combined workflows for large genome assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - LG-WF + tools: [] + update_time: '2021-11-09' + versions: 111 +- create_time: '2021-09-14' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 57321b64220d5835 + latest_version: 20 + license: null + link: https://usegalaxy.org.au/published/workflow?id=57321b64220d5835 + name: 'scRNAseq with AnnData - Step 2: Filtering of low-quality cells and genes, + normalisation, filtering of highly variable genes, scaling.' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - scRNAseq + - single-cell + - transcriptomics + tools: + - anndata_manipulate + - scanpy_filter + - anndata_inspect + - scanpy_normalize + - scanpy_remove_confounders + - scanpy_plot + - scanpy_inspect + update_time: '2021-10-06' + versions: 20 +- create_time: '2021-09-14' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 8055596d732590d6 + latest_version: 29 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8055596d732590d6 + name: 'scRNAseq with AnnData - Step 1: Mitochondria annotation, QC metrics plotting.' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - scRNAseq + - single-cell + - transcriptomics + tools: + - anndata_manipulate + - Cut1 + - anndata_inspect + - tp_replace_in_column + - tp_tail_tool + - tp_awk_tool + - cat1 + - scanpy_plot + - Filter1 + - scanpy_inspect + update_time: '2021-10-06' + versions: 29 +- create_time: '2021-09-14' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 8bc01c1fdd62ad12 + latest_version: 24 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8bc01c1fdd62ad12 + name: 'scRNAseq with AnnData - Step 4: PCA, cell clustering with UMAP, detect marker + genes' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - scRNAseq + - single-cell + - transcriptomics + tools: + - scanpy_plot + - scanpy_cluster_reduce_dimension + - scanpy_inspect + update_time: '2021-10-05' + versions: 24 +- create_time: '2021-09-14' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 106080375ad4eaaa + latest_version: 9 + license: null + link: https://usegalaxy.org.au/published/workflow?id=106080375ad4eaaa + name: ' scRNAseq with AnnData - Step 3: PCA inspection via Elbow plot' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - scRNAseq + - single-cell + - transcriptomics + tools: + - scanpy_plot + - scanpy_cluster_reduce_dimension + update_time: '2021-09-21' + versions: 9 +- create_time: '2021-09-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 94241afd07e8a8b7 + latest_version: 13 + license: null + link: https://usegalaxy.org.au/published/workflow?id=94241afd07e8a8b7 + name: 'scRNAseq preparation with multiple 10X counts datasets - Step 3: Concatenate + datasets' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - scRNAseq + - single-cell + - transcriptomics + tools: + - anndata_manipulate + - __EXTRACT_DATASET__ + - __FILTER_FROM_FILE__ + update_time: '2021-09-21' + versions: 13 +- create_time: '2021-09-08' + creators: [] + doi: '' + edam_operation: + - Community profiling + - Loading + edam_topic: [] + id: 471615c412b305f2 + latest_version: 5 + license: null + link: https://usegalaxy.org.au/published/workflow?id=471615c412b305f2 + name: 'scRNAseq preparation with multiple 10X counts datasets - Step 2: Empty droplets + filtering, import as AnnData.' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - scRNAseq + - 10X + - single-cell + - transcriptomics + tools: + - dropletutils + - anndata_import + update_time: '2021-09-21' + versions: 5 +- create_time: '2021-09-08' + creators: [] + doi: '' + edam_operation: + - Community profiling + - Loading + edam_topic: [] + id: 10296e860e9ef4bb + latest_version: 5 + license: null + link: https://usegalaxy.org.au/published/workflow?id=10296e860e9ef4bb + name: 'scRNAseq preparation with multiple 10X counts datasets - Step 1: Empty droplets + QC Plot' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - scRNAseq + - 10X + - single-cell + - transcriptomics + tools: + - dropletutils + update_time: '2021-09-21' + versions: 5 +- create_time: '2021-05-02' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 738c0e8227519c25 + latest_version: 9 + license: null + link: https://usegalaxy.org.au/published/workflow?id=738c0e8227519c25 + name: BINF90002 workshop 9 - variant calling + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - vcfallelicprimitives + - samtools_idxstats + - bwa_mem + - snpEff + - samtools_flagstat + - freebayes + update_time: '2021-09-08' + versions: 9 +- create_time: '2020-09-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Filtering + - Aggregation + - Scaffolding + - Validation + - Sequence contamination filtering + - Visualisation + - Transcriptome assembly + - Box-Whisker plot plotting + - Sequencing quality control + - Sequence assembly validation + - Scatter plot plotting + edam_topic: [] + id: b7aa22291322e505 + latest_version: 13 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505 + name: Hybrid assembly - Unicycler + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - nanoplot + - fastp + - quast + - unicycler + - filtlong + - multiqc + - busco + update_time: '2021-08-12' + versions: 13 +- create_time: '2020-09-07' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Genome indexing + - Read mapping + - Scaffolding + - Analysis + - Visualisation + - Transcriptome assembly + - Generation + - Cross-assembly + - Mapping assembly + - Read alignment + - Sequence assembly + - Sequence alignment + - Sequence assembly validation + edam_topic: [] + id: 02c74095a7128c9d + latest_version: 18 + license: null + link: https://usegalaxy.org.au/published/workflow?id=02c74095a7128c9d + name: Hybrid assembly - nanopore draft, illumina polishing + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - pilon + - quast + - flye + - busco + - bwa_mem + update_time: '2021-06-04' + versions: 18 +- create_time: '2021-05-08' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Statistical calculation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 52b6fe5af4911b1a + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=52b6fe5af4911b1a + name: Workflow constructed from history 'Unnamed history' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - samtools_view + - vcfvcfintersect + - freebayes + - bwa_mem + update_time: '2021-05-08' + versions: 1 +- create_time: '2021-05-05' + creators: [] + doi: '' + edam_operation: + - Sequence alignment + edam_topic: [] + id: d2073964dbe9acfa + latest_version: 24 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d2073964dbe9acfa + name: Workshop1_2 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - cufflinks + - cuffmerge + - hisat2 + update_time: '2021-05-06' + versions: 24 +- create_time: '2021-05-04' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 55c4d97a08a5ca09 + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=55c4d97a08a5ca09 + name: HISAT workflow test + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - hisat2 + update_time: '2021-05-06' + versions: 3 +- create_time: '2021-05-06' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - Statistical calculation + - RNA-Seq analysis + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 0fc7c14c4d1ac8f5 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=0fc7c14c4d1ac8f5 + name: deans_pipeline + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - fastq_quality_trimmer + - edger + - featurecounts + - deseq2 + - hisat2 + update_time: '2021-05-06' + versions: 1 +- create_time: '2021-05-01' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Sequence alignment + - Nucleic acid sequence analysis + edam_topic: [] + id: 16a2c2e8b3c1ffe6 + latest_version: 7 + license: null + link: https://usegalaxy.org.au/published/workflow?id=16a2c2e8b3c1ffe6 + name: Haiming Li_BINF 6000_workshop 1 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - generate_count_matrix + - jbrowse + - htseq_count + - hisat2 + update_time: '2021-05-06' + versions: 7 +- create_time: '2021-05-05' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Genome indexing + - Sequence composition calculation + - Read mapping + - RNA-Seq analysis + - Transcriptome assembly + - Generation + - Sequence alignment + - Nucleic acid sequence analysis + - Sequencing quality control + edam_topic: [] + id: a35e5a238a70176a + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a35e5a238a70176a + name: Roy_Kanad BINF6000 Workshop 1- Getting data, alignment, quality control, mapping, + quantification, merging assembled transcripts for differential gene analysis + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - stringtie + - bwa + - jbrowse + - htseq_count + - stringtie_merge + - bowtie2 + - hisat2 + update_time: '2021-05-05' + versions: 2 +- create_time: '2021-05-02' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 2a97585556d53a43 + latest_version: 4 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2a97585556d53a43 + name: Workflow constructed from history 'Mazen' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - tophat2 + - cuffmerge + update_time: '2021-05-05' + versions: 4 +- create_time: '2021-05-04' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Nucleic acid sequence analysis + edam_topic: [] + id: b2818098da6e2f82 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b2818098da6e2f82 + name: Workshop1 Australian Site + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - cufflinks + - tophat2 + - cuffmerge + - jbrowse + - htseq_count + update_time: '2021-05-04' + versions: 0 +- create_time: '2021-03-14' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Sequencing quality control + - Sequence analysis + - Formatting + - Box-Whisker plot plotting + - Structural variation detection + - Filtering + - Scatter plot plotting + edam_topic: [] + id: d69a765cfc82a399 + latest_version: 43 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399 + name: Long-read SV calling - human read set workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - SV_calling + tools: + - nanoplot + - samtools_calmd + - sniffles + - picard_SortSam + - samtools_idxstats + - vcfsort + - filtlong + - tp_awk_tool + - minimap2 + update_time: '2021-04-28' + versions: 43 +- create_time: '2020-12-09' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - De-novo assembly + - Genome indexing + - Read mapping + - Coding region prediction + - Analysis + - Genome annotation + - Gene prediction + - Generation + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Read alignment + - Sequence assembly + - Sequence assembly visualisation + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: 7c343e5b55474d19 + latest_version: 20 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19 + name: Chloroplast-genome-assembly-and-annotation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + tools: + - nanoplot + - pilon + - bandage_info + - flye + - fasta-stats + - prokka + - jbrowse + - bandage_image + - bwa_mem + update_time: '2021-04-15' + versions: 20 +- create_time: '2021-02-17' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Phylogenetic tree analysis + - Phylogenetic tree generation + - Multiple sequence alignment + - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree reconstruction + edam_topic: [] + id: a01c3004bcef9dd3 + latest_version: 6 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3 + name: Phylogenetic Tree Building + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - minimap2 + - newick_display + - fasttree + - rbc_mafft + update_time: '2021-04-14' + versions: 6 +- create_time: '2019-03-21' + creators: [] + doi: '' + edam_operation: + - Formatting + edam_topic: [] + id: ca6f29110df8dadc + latest_version: 9 + license: null + link: https://usegalaxy.org.au/published/workflow?id=ca6f29110df8dadc + name: 16S_biodiversity_BIOM + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - MetaDEGalaxy + tools: + - phyloseq_DESeq2 + - symmetricPlot + - phyloseq_richness + - biom_convert + - biom_add_metadata + - phyloseq_taxonomy + - phyloseq_net + - phyloseq_abundance + update_time: '2021-04-01' + versions: 9 +- create_time: '2019-03-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Chimera detection + - Generation + - DNA mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 869440d35a618836 + latest_version: 18 + license: null + link: https://usegalaxy.org.au/published/workflow?id=869440d35a618836 + name: 16S_biodiversity_for_nonoverlap_paired_end + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - MetaDEGalaxy + tools: + - fastqc + - vsearch_search + - trimmomatic + - vsearch_chimera_detection + - biom_convert + - phyloseq_net + - phyloseq_abundance + - phyloseq_DESeq2 + - picard_FilterSamReads + - vsearch_clustering + - cat1 + - phyloseq_richness + - biom_add_metadata + - phyloseq_taxonomy + - addValue + - bwa_mem + - samtools_fastx + - symmetricPlot + - Cut1 + - vsearch_dereplication + - uclust2otutable + - cat_multi_datasets + update_time: '2021-04-01' + versions: 18 +- create_time: '2019-03-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Sequence merging + - Chimera detection + - Generation + - DNA mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 14e80b7f9f68ec2a + latest_version: 16 + license: null + link: https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a + name: 16S_biodiversity_for_overlap_paired_end + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - MetaDEGalaxy + tools: + - fastqc + - vsearch_search + - trimmomatic + - vsearch_chimera_detection + - biom_convert + - iuc_pear + - phyloseq_net + - phyloseq_abundance + - phyloseq_DESeq2 + - picard_FilterSamReads + - vsearch_clustering + - cat1 + - phyloseq_richness + - biom_add_metadata + - phyloseq_taxonomy + - addValue + - bwa_mem + - samtools_fastx + - symmetricPlot + - picard_MergeSamFiles + - Cut1 + - vsearch_dereplication + - uclust2otutable + update_time: '2021-04-01' + versions: 16 +- create_time: '2021-03-08' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Sequencing quality control + - Sequence analysis + - Sequence visualisation + - Box-Whisker plot plotting + - Structural variation detection + - Filtering + - Scatter plot plotting + edam_topic: [] + id: 4871f853090e8be8 + latest_version: 48 + license: null + link: https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8 + name: Long-read SV calling - non-model organism read sets workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - SV_calling + tools: + - nanoplot + - samtools_calmd + - sniffles + - vcfsort + - Extract_features1 + - filtlong + - tp_awk_tool + - tab2fasta + - vcfannotate + - minimap2 + - circos + update_time: '2021-03-22' + versions: 48 +- create_time: '2021-03-21' + creators: [] + doi: '' + edam_operation: + - Sequence visualisation + edam_topic: [] + id: 6588e175004aba38 + latest_version: 21 + license: null + link: https://usegalaxy.org.au/published/workflow?id=6588e175004aba38 + name: Long-read SV calling - circos plots + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - SV_calling + tools: + - tp_awk_tool + - circos + update_time: '2021-03-22' + versions: 21 +- create_time: '2021-03-08' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 142e5f7c1f340838 + latest_version: 23 + license: null + link: https://usegalaxy.org.au/published/workflow?id=142e5f7c1f340838 + name: Long-read SV calling - annotate variant calls + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - SV_calling + tools: + - Extract_features1 + - tp_awk_tool + - vcfannotate + update_time: '2021-03-21' + versions: 23 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - RNA-Seq analysis + - Annotation + edam_topic: [] + id: bdb498b1f0e8944f + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f + name: RNA Seq Counts To Genes + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - annotatemyids + - tp_replace_in_line + - mergeCols1 + - tp_cut_tool + - limma_voom + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1801a8b74c35340f + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1801a8b74c35340f + name: 'CelSeq2: Multi Batch (mm10)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - collection_column_join + - __FLATTEN__ + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - RNA-Seq quantification + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read summarisation + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: a763e53653b10ce0 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a763e53653b10ce0 + name: QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - fastqc + - gtftobed12 + - tp_sort_header_tool + - cutadapt + - rseqc_infer_experiment + - rna_star + - multiqc + - featurecounts + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Pathway or network analysis + - Pathway or network visualisation + - Gene functional annotation + edam_topic: [] + id: 5490661d0153962b + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5490661d0153962b + name: DEG Part - Ref Based RNA Seq - Transcriptomics - GTN + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - deg_annotate + - table_compute + - Cut1 + - Add_a_column1 + - join1 + - goseq + - cat1 + - Grouping1 + - ggplot2_heatmap2 + - ChangeCase + - pathview + - deseq2 + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Gene set testing + - Gene-set enrichment analysis + - Gene functional annotation + edam_topic: [] + id: 9f6e62f465589ca3 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3 + name: RNA Seq Genes To Pathways + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - fgsea + - Cut1 + - tp_sort_header_tool + - Add_a_column1 + - join1 + - tp_cut_tool + - goseq + - egsea + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: af7b95f46485308c + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=af7b95f46485308c + name: RNA Seq Reads To Counts + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - fastqc + - collection_column_join + - samtools_idxstats + - rseqc_read_distribution + - rseqc_geneBody_coverage + - cutadapt + - rseqc_infer_experiment + - multiqc + - picard_MarkDuplicates + - featurecounts + - hisat2 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Sequence alignment + - Sequence composition calculation + - Sequence annotation + - Differential gene expression analysis + - RNA-Seq analysis + - Transcriptome assembly + - Read summarisation + - Sequencing quality control + edam_topic: [] + id: 53010c2f1f207429 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=53010c2f1f207429 + name: De novo transcriptome reconstruction with RNA-Seq + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - fastqc + - trimmomatic + - stringtie + - gffcompare + - deeptools_bam_coverage + - Filter1 + - stringtie_merge + - featurecounts + - deseq2 + - hisat2 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a8d9a16eea69b812 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a8d9a16eea69b812 + name: Visualization Of RNA-Seq Results With Volcano Plot + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - volcanoplot + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Sequence alignment + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 5926a7669eabb1c6 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5926a7669eabb1c6 + name: 'sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - fastqc + - fastq_manipulation + - trim_galore + - bedtools_bamtofastq + - samtool_filter2 + - hisat2 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + edam_topic: [] + id: 3f45685df9b9e792 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=3f45685df9b9e792 + name: 'sRNA Seq Step 2: Salmon And DESeq2' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - Filter1 + - deseq2 + - salmon + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 4a7f22081ecde089 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=4a7f22081ecde089 + name: Blockclust 1.1.0 Clustering + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - samtools_sort + - blockclust + - blockbuster + - tp_sort_header_tool + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + - RNA-Seq analysis + - Pathway or network analysis + edam_topic: [] + id: 6a161c87d19a543c + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=6a161c87d19a543c + name: Workflow Constructed From History 'Heinz Workflow Trial Sep 11' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - heinz_bum + - heinz + - Cut1 + - heinz_visualization + - heinz_scoring + - deseq2 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f7fd24318c4bf949 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f7fd24318c4bf949 + name: Heatmap2 Workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - ggplot2_heatmap2 + - datamash_transpose + - join1 + - Cut1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Gene-set enrichment analysis + edam_topic: [] + id: d04b26372b28e8ed + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d04b26372b28e8ed + name: GO Enrichment Workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - goenrichment + - goslimmer + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence trimming + - Sequence composition calculation + - Read pre-processing + - Primer removal + - Sequencing quality control + edam_topic: [] + id: 7ba13e928de65e61 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7ba13e928de65e61 + name: GTN - Sequence Analyses - Quality Control + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - sequence-analysis + - galaxy-training-network + tools: + - fastqc + - multiqc + - cutadapt + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 0a477899db53d098 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=0a477899db53d098 + name: GTN - Sequence Analyses - Mapping + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - sequence-analysis + - galaxy-training-network + tools: + - fastqc + - trim_galore + - bamFilter + - samtools_stats + - multiqc + - bowtie2 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Sequence composition calculation + - Read mapping + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: c456492ce4f963d0 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c456492ce4f963d0 + name: GTN - Sequence Analyses - Mapping - Jbrowse + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - sequence-analysis + - galaxy-training-network + tools: + - fastqc + - trim_galore + - samtools_stats + - jbrowse + - multiqc + - bowtie2 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 2a6324600f159061 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2a6324600f159061 + name: 'Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With + Mothur]' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - mothur_remove_groups + - mothur_count_groups + - mothur_cluster_split + - mothur_make_shared + - mothur_sub_sample + - mothur_classify_otu + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 58bd08b1530e7cae + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=58bd08b1530e7cae + name: 'Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis + With Mothur]' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - mothur_rarefaction_single + - mothur_dist_seqs + - mothur_make_shared + - mothur_cluster + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 7e381c150820e506 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7e381c150820e506 + name: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With + Mothur]' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - mothur_summary_seqs + - mothur_classify_seqs + - mothur_remove_lineage + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 1954437da1e0c4de + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1954437da1e0c4de + name: 'Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With + Mothur]' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - mothur_screen_seqs + - mothur_unique_seqs + - mothur_summary_seqs + - mothur_count_seqs + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 832fe9dfc67fd8ed + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=832fe9dfc67fd8ed + name: 'Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial + Analysis With Mothur]' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_remove_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_unique_seqs + - mothur_pre_cluster + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 5877e2d5eba79f36 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5877e2d5eba79f36 + name: 'Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With + Mothur]' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - mothur_summary_single + - XY_Plot_1 + - mothur_rarefaction_single + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: a52609119b30e64d + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a52609119b30e64d + name: 'Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - collapse_dataset + - mothur_heatmap_sim + - mothur_dist_shared + - mothur_tree_shared + - newick_display + - mothur_venn + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence alignment analysis + - Sequence composition calculation + - Sequence comparison + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence similarity search + - Sequencing quality control + edam_topic: [] + id: 408a31694e9c85e6 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6 + name: 'Workflow 1: Preprocessing [Metatranscriptomics]' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - fastqc + - fastq_paired_end_interlacer + - cutadapt + - multiqc + - bg_sortmerna + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Phylogenetic tree generation + - Visualisation + - Sequence clustering + - Phylogenetic tree analysis + - DNA barcoding + - Phylogenetic tree reconstruction + - Sequencing quality control + edam_topic: [] + id: 2717e90438c7fb8c + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c + name: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - mothur_heatmap_sim + - mothur_make_biom + - mothur_cluster + - mothur_rarefaction_single + - mothur_align_seqs + - mothur_classify_seqs + - mothur_venn + - taxonomy_krona_chart + - mothur_get_groups + - mothur_seq_error + - mothur_make_shared + - newick_display + - mothur_remove_groups + - mothur_summary_seqs + - mothur_filter_seqs + - mothur_dist_shared + - mothur_dist_seqs + - mothur_chimera_vsearch + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_tree_shared + - mothur_unique_seqs + - mothur_classify_otu + - mothur_taxonomy_to_krona + - mothur_remove_lineage + - mothur_remove_seqs + - mothur_summary_single + - XY_Plot_1 + - mothur_count_groups + - mothur_cluster_split + - mothur_sub_sample + - mothur_pre_cluster + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 74bd939615090c2c + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=74bd939615090c2c + name: Amplicon Tutorial + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - mothur_summary_seqs + - mothur_make_group + - mothur_filter_seqs + - krona-text + - mothur_screen_seqs + - mothur_count_seqs + - mothur_cluster_split + - mothur_make_biom + - mothur_merge_files + - mothur_make_shared + - mothur_unique_seqs + - mothur_align_seqs + - mothur_classify_otu + - mothur_classify_seqs + - mothur_pre_cluster + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 3678781bf7619a89 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89 + name: MSI Finding Diff Analytes + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metabolomics + - galaxy-training-network + tools: + - cardinal_combine + - cardinal_mz_images + - cardinal_classification + - cardinal_segmentations + - cardinal_preprocessing + - cardinal_quality_report + - maldi_quant_preprocessing + - Grep1 + - join_files_on_column_fuzzy + - Summary_Statistics1 + - maldi_quant_peak_detection + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: fa0243ff9b5ca997 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=fa0243ff9b5ca997 + name: 'Workflow Constructed From History ''imported: testpourGCC''' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metabolomics + - galaxy-training-network + tools: + - xcms_merge + - abims_xcms_fillPeaks + - abims_xcms_retcor + - generic_filter + - abims_xcms_group + - Univariate + - wsdl_hmdb + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - Batch_correction + - quality_metrics + - xcms_plot_chromatogram + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: a9e52a40b63d26fc + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a9e52a40b63d26fc + name: Galaxy Intro Strands 2 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - introduction + - galaxy-training-network + tools: + - gene2exon1 + - tp_cat + - gops_intersect_1 + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: f27f6ed478d7a258 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f27f6ed478d7a258 + name: Galaxy Intro Strands + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - introduction + - galaxy-training-network + tools: + - tp_cat + - gops_intersect_1 + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: 1d1c2589f94fc4df + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1d1c2589f94fc4df + name: 'GTN Training: Galaxy 101 For Everyone' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - introduction + - galaxy-training-network + tools: + - Remove beginning1 + - Cut1 + - csv_to_tabular + - datamash_ops + - Grouping1 + - tp_sorted_uniq + - ggplot2_point + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: b46bc04e0418fdfa + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b46bc04e0418fdfa + name: Galaxy Intro Short + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - introduction + - galaxy-training-network + tools: + - fastqc + - cshl_fastq_quality_filter + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 62548740196799c3 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=62548740196799c3 + name: Analyze Screen + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - imaging + - galaxy-training-network + tools: + - collapse_dataset + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Gene prediction + - Genome annotation + - Genome visualisation + - Coding region prediction + edam_topic: [] + id: 33401b29d277b447 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=33401b29d277b447 + name: Genome Annotation with Prokka [Feb 2020] + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - genome-annotation + - galaxy-training-network + tools: + - prokka + - jbrowse + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 05e4ef85cbf0dc20 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=05e4ef85cbf0dc20 + name: Select First N Lines + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - galaxy-interface + - galaxy-training-network + tools: + - tp_head_tool + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c4a303c1571d202e + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c4a303c1571d202e + name: Tutorial workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - galaxy-interface + - galaxy-training-network + tools: + - tp_tac + - Show beginning1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: da28ceaaeae16c57 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=da28ceaaeae16c57 + name: Subworkflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - galaxy-interface + - galaxy-training-network + tools: + - Paste1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c06b569f044b971f + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c06b569f044b971f + name: Phenology "stacked" Visualization Creation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ecology + - galaxy-training-network + tools: + - Paste1 + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 404f9b6343bd1294 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=404f9b6343bd1294 + name: Abundance Index "stacked" Visualization Creation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ecology + - galaxy-training-network + tools: + - Paste1 + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence trimming + - Data handling + - Sequence file editing + - Read pre-processing + - Read mapping + - Primer removal + edam_topic: [] + id: 79ca45e45d76871f + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=79ca45e45d76871f + name: MakeAFakeInput + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - contributing + - galaxy-training-network + tools: + - Cut1 + - tp_cat + - random_lines1 + - bam_to_sam + - tp_cut_tool + - tp_sed_tool + - cutadapt + - fastq_to_tabular + - tp_sorted_uniq + - seqtk_subseq + - bowtie2 + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 902e270d424f0e8c + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=902e270d424f0e8c + name: Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - computational-chemistry + - galaxy-training-network + tools: + - rdock_rbcavity + - split_file_to_collection + - collapse_dataset + - ctb_frankenstein_ligand + - enumerate_charges + - xchem_pose_scoring + - sucos_max_score + - rdock_rbdock + - openbabel_compound_convert + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Read mapping + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Sequence file editing + - Sequencing quality control + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: fc3c83b11f527977 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977 + name: assembly_with_preprocessing_and_sra_download + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + - galaxy-training-network + tools: + - samtools_fastx + - fasta_filter_by_length + - nanoplot + - fastp + - samtools_view + - bandage_info + - collapse_dataset + - unicycler + - fasterq_dump + - __ZIP_COLLECTION__ + - bandage_image + - samtools_stats + - minimap2 + - multiqc + - bowtie2 + - seqtk_sample + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Data handling + - Genome assembly + - Read mapping + - Aggregation + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Sequence file editing + - Sequencing quality control + - Sequence assembly visualisation + - Scatter plot plotting + edam_topic: [] + id: b59fada651043735 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b59fada651043735 + name: assembly_with_preprocessing + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + - galaxy-training-network + tools: + - samtools_fastx + - fasta_filter_by_length + - nanoplot + - fastp + - samtools_view + - bandage_info + - collapse_dataset + - unicycler + - __ZIP_COLLECTION__ + - bandage_image + - samtools_stats + - minimap2 + - multiqc + - bowtie2 + - seqtk_sample + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence visualisation + edam_topic: [] + id: 0f9a29e8eac2075c + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=0f9a29e8eac2075c + name: Workflow constructed from history 'Workflow constructed from history 'Workflow + constructed from history 'Circos tutorial''' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - visualisation + - galaxy-training-network + tools: + - Remove beginning1 + - Cut1 + - random_lines1 + - Grep1 + - circos + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Sequence visualisation + edam_topic: [] + id: 6a58898d37da5c83 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=6a58898d37da5c83 + name: Workflow constructed from history 'Nature workflow' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - visualisation + - galaxy-training-network + tools: + - circos + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3e6f755ee62f7301 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=3e6f755ee62f7301 + name: Calling variants in non-diploid systems + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - galaxy-training-network + tools: + - fastqc + - picard_MergeSamFiles + - Cut1 + - bamFilter + - vcffilter2 + - vcf2tsv + - bamleftalign + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Validation + - Formatting + - Data handling + - Sequencing quality control + edam_topic: [] + id: b08342866a118a5e + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b08342866a118a5e + name: QC report + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - multiqc + - picard_MarkDuplicates + - rseqc_infer_experiment + - samtools_idxstats + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Validation + - Community profiling + - Sequence alignment + - Loading + - Sequencing quality control + edam_topic: [] + id: f627023a3401bf9b + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f627023a3401bf9b + name: Pre-processing of 10X Single-Cell RNA Datasets + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - single-cell + - galaxy-training-network + tools: + - multiqc + - rna_starsolo + - dropletutils + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Prediction and recognition + edam_topic: [] + id: f9f685d6150e48c5 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5 + name: Metaproteomics_GTN + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - query_tabular + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 59c9a6efaf57ce35 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=59c9a6efaf57ce35 + name: 'Proteomics: Peptide and Protein ID using OpenMS' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - FalseDiscoveryRate + - FidoAdapter + - XTandemAdapter + - PeakPickerHiRes + - FileInfo + - TextExporter + - Grep1 + - IDPosteriorErrorProbability + - PeptideIndexer + - IDScoreSwitcher + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Query and retrieval + - Statistical inference + - Quantification + - Filtering + - Indexing + - Heat map generation + - Functional clustering + - Visualisation + - Differential protein expression analysis + - Principal component visualisation + edam_topic: [] + id: f8183bba3a1d150d + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d + name: metaquantome-taxonomy-workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - metaquantome_stat + - metaquantome_viz + - metaquantome_sample + - metaquantome_expand + - metaquantome_filter + - metaquantome_db + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Peptide database search + - Conversion + edam_topic: [] + id: 1b9bfe7ce484fdc2 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2 + name: GTN Proteogemics2 Database Search + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - query_tabular + - mz_to_sqlite + - tab2fasta + - peptide_shaker + - search_gui + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Variant calling + - RNA-Seq analysis + - Transcriptome assembly + - Statistical calculation + - Sequence alignment + - Sequence annotation + edam_topic: [] + id: 7cd4fcc8e06ce4fd + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd + name: GTN Proteogenomics1 Database Creation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - filter_tabular + - tp_cat + - stringtie + - fasta2tab + - query_tabular + - regexColumn1 + - fasta_merge_files_and_filter_unique_sequences + - bed_to_protein_map + - tp_replace_in_column + - hisat2 + - gffcompare + - tab2fasta + - gffcompare_to_bed + - custom_pro_db + - sqlite_to_tabular + - translate_bed + - freebayes + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Tag-based peptide identification + - Heat map generation + - Spectrum calculation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Differential protein expression profiling + - Clustering + - Principal component plotting + edam_topic: [] + id: 1727d16fa4dec19c + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c + name: 'Proteomics: MaxQuant and MSstats LFQ workflow' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - uniprot + - maxquant + - Remove beginning1 + - Cut1 + - datamash_ops + - fasta2tab + - ggplot2_heatmap + - ggplot2_heatmap2 + - tp_replace_in_column + - tp_easyjoin_tool + - Grep1 + - cat1 + - msstats + - Summary_Statistics1 + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7cddb345877f08bf + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf + name: 'Proteomics: database handling including mycoplasma' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - DecoyDatabase + - tab2fasta + - addValue + - dbbuilder + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 65a659982f955743 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=65a659982f955743 + name: 'Proteomics: database handling' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - DecoyDatabase + - tab2fasta + - addValue + - dbbuilder + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: da79aa2dfd6b34bc + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc + name: 'Proteomics: Peptide and Protein Quantification via stable istobe labeling' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - FalseDiscoveryRate + - IDConflictResolver + - histogram_rpy + - FidoAdapter + - XTandemAdapter + - MultiplexResolver + - FeatureFinderMultiplex + - FileInfo + - TextExporter + - IDMapper + - ProteinQuantifier + - tp_tail_tool + - Grep1 + - IDPosteriorErrorProbability + - Summary_Statistics1 + - PeptideIndexer + - IDScoreSwitcher + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Query and retrieval + - Statistical inference + - Quantification + - Filtering + - Indexing + - Heat map generation + - Functional clustering + - Visualisation + - Differential protein expression analysis + - Principal component visualisation + edam_topic: [] + id: cada735fa0716570 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=cada735fa0716570 + name: metaquantome-function-worklow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - metaquantome_stat + - metaquantome_viz + - metaquantome_sample + - metaquantome_expand + - metaquantome_filter + - metaquantome_db + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: 781457327e644c7e + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=781457327e644c7e + name: 'Proteomics: MaxQuant workflow' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - maxquant + - Cut1 + - tp_sort_header_tool + - Add_a_column1 + - Grep1 + - histogram_rpy + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c049ae8f729b2d7e + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c049ae8f729b2d7e + name: GTN Proteogemics3 Novel Peptide Analysis + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - query_tabular + - ncbi_blastp_wrapper + - peptide_genomic_coordinate + - pep_pointer + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Statistical calculation + - Visualisation + - Taxonomic classification + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: 4c7e0703aace6aa3 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=4c7e0703aace6aa3 + name: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metagenomics + - galaxy-training-network + tools: + - fastqc + - fastp + - taxonomy_krona_chart + - Remove beginning1 + - tp_replace_in_line + - kraken2 + - porechop + - datamash_reverse + - multiqc + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 80cf8be8c8bf384a + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=80cf8be8c8bf384a + name: 'MSI Workflow: spatial distribution' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - metabolomics + - galaxy-training-network + tools: + - cardinal_filtering + - cardinal_mz_images + - cardinal_quality_report + - cardinal_data_exporter + - cardinal_spectra_plots + - Filter1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 252baad4e5ade6bc + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=252baad4e5ade6bc + name: Find exons with the highest number of interactions + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - introduction + - galaxy-training-network + tools: + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - comp1 + - Show beginning1 + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Formatting + - Data handling + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 51b745f8c964e5c6 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=51b745f8c964e5c6 + name: NGS_tutorial + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - introductions + - galaxy-training-network + tools: + - fastp + - multiqc + - snpSift_extractFields + - collapse_dataset + - lofreq_call + - fasterq_dump + - lofreq_indelqual + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 19e3488987d58d73 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=19e3488987d58d73 + name: Galaxy Introduction Peaks2Genes - Part 1 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - introduction + - galaxy-training-network + tools: + - get_flanks1 + - CONVERTER_interval_to_bed_0 + - gops_intersect_1 + - Grouping1 + - tp_tail_tool + - tp_replace_in_column + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Visualisation + - Image annotation + - Data handling + - Image analysis + edam_topic: [] + id: 2a1e4de0dc77bbed + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed + name: 'GTN Training: Introduction To Imaging' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - imaging + - galaxy-training-network + tools: + - ip_imageinfo + - unzip + - ip_convertimage + - ip_threshold + - ip_count_objects + - ip_overlay_segmentation + - ip_binary_to_labelimage + - ip_filter_standard + - ip_histogram_equalization + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Enrichment analysis + - Gene regulatory network analysis + - Peak calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2b0a986519532412 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2b0a986519532412 + name: Identification of the binding sites of the T-cell acute lymphocytic leukemia + protein 1 (TAL1) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - epigenetics + - galaxy-training-network + tools: + - fastqc + - trimmomatic + - samtools_idxstats + - deeptools_plot_heatmap + - deeptools_bam_compare + - deeptools_compute_matrix + - bwa + - deeptools_plot_fingerprint + - deeptools_multi_bam_summary + - bedtools_intersectbed + - deeptools_plot_correlation + - macs2_callpeak + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 28cf646b95e4d3ab + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=28cf646b95e4d3ab + name: MD protein-ligand workflow (from PDB structure) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - cheminformatics + - moleculardynamics + - computational-chemistry + - galaxy-training-network + tools: + - get_pdb + - ambertools_acpype + - gmx_sim + - gmx_editconf + - gmx_em + - gmx_setup + - tp_grep_tool + - gmx_solvate + - gmx_merge_topology_files + - openbabel_compound_convert + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 5add59b908662af0 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5add59b908662af0 + name: Workflow constructed from history 'Hsp90-MDAnalysis' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - computational-chemistry + - galaxy-training-network + tools: + - bio3d_rmsf + - bio3d_rmsd + - bio3d_pca + - mdanalysis_cosine_analysis + - vmd_hbonds + - md_converter + - bio3d_pca_visualize + - gmx_editconf + update_time: '2021-03-19' + versions: 0 +- create_time: '2021-03-19' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - De-novo assembly + - Genome indexing + - Read mapping + - Coding region prediction + - Analysis + - Genome annotation + - Gene prediction + - Generation + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Read alignment + - Sequence assembly + - Sequence assembly visualisation + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: b5403e4fff2961f9 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9 + name: Chloroplast-genome-assembly-and-annotation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + - galaxy-training-network + tools: + - nanoplot + - pilon + - bandage_info + - flye + - fasta-stats + - prokka + - jbrowse + - bandage_image + - bwa_mem + update_time: '2021-03-19' + versions: 0 +- create_time: '2019-02-11' + creators: [] + doi: '' + edam_operation: + - Phylogenetic analysis + - Sequence analysis + - Phylogenetic tree analysis + - Genome assembly + - Phylogenetic tree generation + - Phylogenetic tree reconstruction + edam_topic: [] + id: 3fd2195b6928d5e0 + latest_version: 13 + license: null + link: https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0 + name: SIH_pangenome_phylogeny + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - newick_display + - iqtree + - roary + update_time: '2021-03-11' + versions: 13 +- create_time: '2021-03-10' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3c1b1f210c7c292b + latest_version: 24 + license: null + link: https://usegalaxy.org.au/published/workflow?id=3c1b1f210c7c292b + name: BINF90002 Workshop Week 2 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - fastp + - picard_SortSam + - samtools_idxstats + - bwa + - multiqc + update_time: '2021-03-10' + versions: 24 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 2546c9599794a99a + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2546c9599794a99a + name: 'SARS-CoV-2: downsample ONT reads assigned to transcripts' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ONT + - covid19.galaxyproject.org + tools: + - samtools_view + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: 0b0957d7cbab16c0 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=0b0957d7cbab16c0 + name: 'SARS-CoV-2: classify ONT reads by transcript junction' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ONT + - covid19.galaxyproject.org + tools: + - tp_text_file_with_recurring_lines + - Cut1 + - split_file_to_collection + - collapse_dataset + - __BUILD_LIST__ + - __RELABEL_FROM_FILE__ + - cat1 + - bedtools_intersectbed + - tp_head_tool + - tp_replace_in_column + - samtools_view + - param_value_from_file + - __MERGE_COLLECTION__ + - createInterval + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: + - Pairwise sequence alignment + - Formatting + edam_topic: [] + id: fba0eb562a710733 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=fba0eb562a710733 + name: 'SARS-CoV-2: map ONT reads to transcripts' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ONT + - covid19.galaxyproject.org + tools: + - samtools_fastx + - picard_NormalizeFasta + - filter_by_fasta_ids + - minimap2 + - samtools_view + - deeptools_bam_coverage + update_time: '2021-03-03' + versions: 2 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: + - Mapping + edam_topic: [] + id: e154a9b605ea0886 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886 + name: 'COVID-19: consensus construction' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - gops_concat_1 + - Cut1 + - collapse_dataset + - bedtools_genomecoveragebed + - Add_a_column1 + - gops_merge_1 + - gops_subtract_1 + - bedtools_maskfastabed + - vcf2tsv + - compose_text_param + - tp_find_and_replace + - bcftools_consensus + - Filter1 + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 76bb6bde19975e05 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=76bb6bde19975e05 + name: 'COVID-19: Variation analysis for PE RNASeq Illumina data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID19 + - RNASeq + - PE + - Illumina + - Fastq->VCF + tools: + - fastp + - multiqc + - Cut1 + - collapse_dataset + - lofreq_call + - lofreq_indelqual + - tp_grep_tool + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - __FILTER_FROM_FILE__ + - picard_MarkDuplicates + - samtools_view + - Filter1 + - lofreq_viterbi + - bwa_mem + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - Pairwise sequence alignment + - SNP detection + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 0c6f7bfc826433c4 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=0c6f7bfc826433c4 + name: 'COVID-19: variation analysis of ARTIC ONT data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - lofreq_filter + - tp_find_and_replace + - minimap2 + - samtools_view + - snpeff_sars_cov_2 + - multiqc + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 7fd58f5fc93f414e + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7fd58f5fc93f414e + name: 'COVID-19: variation analysis on ARTIC PE data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bd1cf22d47389742 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=bd1cf22d47389742 + name: 'COVID-19: variation analysis on WGS PE data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: 31dbd313e5c8160b + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=31dbd313e5c8160b + name: 'COVID-19: variation analysis on WGS SE data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-03-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8e2b94c6fbf44368 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8e2b94c6fbf44368 + name: 'COVID-19: variation analysis reporting' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - split_file_to_collection + - tp_sort_header_tool + - datamash_ops + - tp_easyjoin_tool + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2021-03-03' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 7a0b3968968c5994 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=7a0b3968968c5994 + name: 'COVID-19: variation analysis reporting' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - snpSift_filter + - snpSift_extractFields + - Cut1 + - collapse_dataset + - Add_a_column1 + - tp_sort_header_tool + - tp_split_on_column + - datamash_ops + - tp_easyjoin_tool + - tp_tail_tool + - tp_head_tool + - cat1 + - snpfreqplot + - compose_text_param + - replace_column_with_key_value_file + - tp_find_and_replace + - Filter1 + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - SNP detection + - Formatting + - Read mapping + - Sequencing quality control + edam_topic: [] + id: a29670ff0ecb1a38 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a29670ff0ecb1a38 + name: 'COVID-19: variation analysis on WGS SE data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bowtie2 + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: e439a0e17a90d24c + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e439a0e17a90d24c + name: 'COVID-19: variation analysis on ARTIC PE data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - covid19.galaxyproject.org + tools: + - fastp + - vcfvcfintersect + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: fedf2874752ac1f6 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=fedf2874752ac1f6 + name: 'COVID-19: variation analysis on WGS PE data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - covid19.galaxyproject.org + tools: + - fastp + - multiqc + - lofreq_call + - lofreq_indelqual + - lofreq_filter + - samtools_stats + - snpeff_sars_cov_2 + - samtools_view + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-02-22' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Base-calling + - Variant calling + - Sequence contamination filtering + - Pairwise sequence alignment + - SNP detection + - Validation + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: 47ce6a2d30887637 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=47ce6a2d30887637 + name: 'COVID-19: variation analysis of ARTIC ONT data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + - ONT + - covid19.galaxyproject.org + tools: + - fastp + - medaka_consensus + - medaka_variant + - ivar_trim + - qualimap_bamqc + - samtools_stats + - bamleftalign + - __FLATTEN__ + - lofreq_filter + - tp_find_and_replace + - minimap2 + - samtools_view + - snpeff_sars_cov_2 + - multiqc + update_time: '2021-02-22' + versions: 1 +- create_time: '2021-01-15' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 8ffcaa3f4a56ce35 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8ffcaa3f4a56ce35 + name: D. silvarum workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - samtools_slice_bam + - ivar_consensus + - bwa_mem + update_time: '2021-02-14' + versions: 2 +- create_time: '2020-12-29' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 265a3ce9305702f5 + latest_version: 7 + license: null + link: https://usegalaxy.org.au/published/workflow?id=265a3ce9305702f5 + name: H. asiaticum workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - samtools_slice_bam + - ivar_consensus + - bwa_mem + update_time: '2021-02-14' + versions: 7 +- create_time: '2021-01-12' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 71f90428fbf8755b + latest_version: 10 + license: null + link: https://usegalaxy.org.au/published/workflow?id=71f90428fbf8755b + name: R. sanguineus workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - samtools_slice_bam + - ivar_consensus + - bwa_mem + update_time: '2021-02-14' + versions: 10 +- create_time: '2020-12-08' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome assembly + - De-novo assembly + - Genome indexing + - Read mapping + - Analysis + - Generation + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Read alignment + - Sequence assembly + - Sequence assembly visualisation + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: 22bd45f60c60a338 + latest_version: 4 + license: null + link: https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338 + name: combined-workflows-sweet-potato-assembly-to-annotation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + tools: + - nanoplot + - pilon + - bandage_info + - flye + - fasta-stats + - jbrowse + - bandage_image + - bwa_mem + update_time: '2020-12-08' + versions: 4 +- create_time: '2020-01-10' + creators: [] + doi: '' + edam_operation: + - Genome assembly + - De-novo assembly + - Genome indexing + - Read mapping + - Analysis + - Generation + - Box-Whisker plot plotting + - Cross-assembly + - Mapping assembly + - Read alignment + - Sequence assembly + - Sequence assembly visualisation + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: 2cb16d321a804b1a + latest_version: 10 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a + name: workflow-sweet-potato-assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + tools: + - nanoplot + - pilon + - bandage_info + - flye + - fasta-stats + - bandage_image + - bwa_mem + update_time: '2020-12-08' + versions: 10 +- create_time: '2020-01-10' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + edam_topic: [] + id: 0dbb0d1ae1222bd0 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=0dbb0d1ae1222bd0 + name: workflow-sweet-potato-annotation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + tools: + - jbrowse + update_time: '2020-12-08' + versions: 2 +- create_time: '2020-01-10' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 59d6ee23bff41eec + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=59d6ee23bff41eec + name: workflow-sweet-potato-viewreads + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + tools: + - jbrowse + - bwa_mem + update_time: '2020-12-08' + versions: 2 +- create_time: '2020-10-14' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq quantification + - Gene expression analysis + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: b0614274c66efa95 + latest_version: 4 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b0614274c66efa95 + name: Galaxy proof-of-concept + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - salmon + - fastqc + - collapse_dataset + update_time: '2020-10-19' + versions: 4 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 04f6ad62f34313ea + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=04f6ad62f34313ea + name: MS Imaging Loading Exploring Data + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - Grep1 + - cardinal_quality_report + - tp_sort_header_tool + - cardinal_data_exporter + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Heat map generation + - Standardisation and normalisation + - Protein quantification + - Visualisation + - Imputation + - Clustering + - Principal component plotting + edam_topic: [] + id: 43a951ec514498f6 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6 + name: Maxquant_lfq_serum + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - maxquant + - Cut1 + - tp_sort_header_tool + - Add_a_column1 + - histogram_rpy + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 236e0f306916149b + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=236e0f306916149b + name: Tails Triple Dimethyl OpenMS2.1 + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - HighResPrecursorMassCorrector + - FalseDiscoveryRate + - IDConflictResolver + - IDFilter + - IDMerger + - FeatureFinderMultiplex + - ConsensusID + - MSGFPlusAdapter + - IDMapper + - FileFilter + - MzTabExporter + - PeptideIndexer + - FileMerger + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c2f449e69d06ccf5 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5 + name: ProteinID SG PS Tutorial WF datasetCollection + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - PeakPickerHiRes + - FileConverter + - Grep1 + - peptide_shaker + - search_gui + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 33922db405a97cbb + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb + name: Peptide And Protein ID Tutorial + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - PeakPickerHiRes + - FileConverter + - Grep1 + - peptide_shaker + - search_gui + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 03efeb2948494130 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=03efeb2948494130 + name: Peptide And Protein ID Via OMS Using Two Search Engines + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - FalseDiscoveryRate + - IDFilter + - FidoAdapter + - XTandemAdapter + - IDMerger + - PeptideIndexer + - FileInfo + - MSGFPlusAdapter + - IDPosteriorErrorProbability + - ConsensusID + - IDScoreSwitcher + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 88fa3e250db2d70e + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=88fa3e250db2d70e + name: Protein ID Workflow For Galaxy Training + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - proteomics + - galaxy-training-network + tools: + - IDFilter + - FidoAdapter + - XTandemAdapter + - PeptideIndexer + - FileInfo + - TextExporter + - Grep1 + - IDPosteriorErrorProbability + - FalseDiscoveryRate + - IDScoreSwitcher + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 517f947adc81a16a + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=517f947adc81a16a + name: ml_classification + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - statistics + - classification + - ml + - cheminformatics + - galaxy-training-network + tools: + - Remove beginning1 + - sklearn_build_pipeline + - sklearn_estimator_attributes + - sklearn_ensemble + - plotly_ml_performance_plots + - sklearn_svm_classifier + - sklearn_generalized_linear + - sklearn_nn_classifier + - sklearn_searchcv + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: + - Visualisation + edam_topic: [] + id: d858cfd9303bb99a + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d858cfd9303bb99a + name: Clustering in Machine Learning + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - statistics + - clustering + - ml + - galaxy-training-network + tools: + - ggplot2_point + - sklearn_numeric_clustering + - csv_to_tabular + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Taxonomic classification + - Phylogenetic tree generation + - Sequence composition calculation + - Phylogenetic tree visualisation + - Variant calling + - Validation + - Antimicrobial resistance prediction + - Sequencing quality control + edam_topic: [] + id: 5693811cd933d2a2 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2 + name: M. tuberculosis Variant Analysis tutorial + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - prokaryote + - galaxy-training-network + tools: + - fastqc + - trimmomatic + - snippy + - tbvcfreport + - kraken2 + - jbrowse + - tb_variant_filter + - multiqc + - tb_profiler_profile + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: + - Formatting + - Data handling + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 30a601039d24e2eb + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=30a601039d24e2eb + name: Simple COVID-19 - PE Variation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - galaxy-training-network + tools: + - fastp + - snpSift_extractFields + - lofreq_call + - fasterq_dump + - lofreq_indelqual + - samtools_stats + - snpeff_sars_cov_2 + - multiqc + - picard_MarkDuplicates + - lofreq_viterbi + - bwa_mem + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: + - Sequence visualisation + edam_topic: [] + id: f85353f93461d180 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f85353f93461d180 + name: Visualisation with Circos + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - visualisation + - galaxy-training-network + tools: + - circos + update_time: '2020-08-31' + versions: 1 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Sequence composition calculation + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Sequence trimming + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: daff6854b5dfc6f1 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=daff6854b5dfc6f1 + name: GTN - ChIP Seq - Formation Of Super Structures On Xi + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - epigenetics + - galaxy-training-network + tools: + - fastqc + - deeptools_plot_fingerprint + - deeptools_bam_coverage + - bowtie2 + - gops_concat_1 + - samtools_idxstats + - tp_sort_header_tool + - deeptools_bam_compare + - datamash_ops + - trim_galore + - cat1 + - bedtools_mergebed + - Add_a_column1 + - macs2_callpeak + - Filter1 + - deeptools_plot_heatmap + - deeptools_compute_matrix + - deeptools_multi_bam_summary + - bedtools_intersectbed + - bedtools_sortbed + - deeptools_plot_correlation + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 91c8daa5f2bcf7c0 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0 + name: Workflow Methylation Seq + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - epigenetics + - galaxy-training-network + tools: + - fastqc + - pileometh + - deeptools_compute_matrix + - metilene + - tp_tail_tool + - tp_awk_tool + - replace_column_with_key_value_file + - bwameth + - deeptools_plot_profile + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-08-31' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Sequence composition calculation + - Mapping + - Read mapping + - Enrichment analysis + - Primer removal + - Gene regulatory network analysis + - Sequence trimming + - Visualisation + - Peak calling + - Read pre-processing + - Sequencing quality control + edam_topic: [] + id: 99821674db7682bb + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=99821674db7682bb + name: ATAC-seq GTM + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - epigenetics + - galaxy-training-network + tools: + - fastqc + - deeptools_plot_heatmap + - bedtools_bamtobed + - samtools_sort + - deeptools_compute_matrix + - bamFilter + - pygenomeTracks + - bedtools_sortbed + - cutadapt + - picard_CollectInsertSizeMetrics + - genrich + - tp_awk_tool + - macs2_callpeak + - wig_to_bigWig + - picard_MarkDuplicates + - bowtie2 + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree visualisation + - Genome visualisation + - Variant calling + - Phylogenetic tree generation + edam_topic: [] + id: 1719e0eb54b41f68 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1719e0eb54b41f68 + name: Microbial Variant Calling + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - galaxy-training-network + tools: + - jbrowse + - snippy + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Sequence analysis + - Statistical calculation + - Genetic variation analysis + edam_topic: [] + id: ac89c2d51c32cc9c + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=ac89c2d51c32cc9c + name: Diploid + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - galaxy-training-network + tools: + - vcfallelicprimitives + - gemini_load + - gemini_db_info + - gemini_query + - snpEff_download + - snpEff + - freebayes + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: e66306b1006d010b + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e66306b1006d010b + name: Mapping And Molecular Identification Of Phenotype Causing Mutations + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - galaxy-training-network + tools: + - mimodd_vcf_filter + - mimodd_varcall + - mimodd_map + - snpEff + - snpEff_download + - mimodd_varreport + - tp_find_and_replace + - mimodd_varextract + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 2362ff8880213586 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=2362ff8880213586 + name: Calling variants in non-diploid systems + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - galaxy-training-network + tools: + - fastqc + - picard_MergeSamFiles + - Cut1 + - bamFilter + - vcffilter2 + - vcf2tsv + - bamleftalign + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome indexing + - Sequence composition calculation + - Read mapping + - Validation + - Variant calling + - Sequence analysis + - Generation + - Sequence alignment + - Genetic variation analysis + - Sequencing quality control + edam_topic: [] + id: 5442f0437ade82c4 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=5442f0437ade82c4 + name: Exome Seq Training Full W Cached Ref + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - galaxy-training-network + tools: + - fastqc + - gemini_inheritance + - gemini_load + - samtools_rmdup + - bcftools_norm + - snpEff + - multiqc + - samtool_filter2 + - freebayes + - bwa_mem + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-04-17' + creators: [] + doi: '' + edam_operation: + - Variant calling + - Sequence analysis + - Statistical calculation + - Genetic variation analysis + edam_topic: [] + id: 1be22b394f9ec3ab + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1be22b394f9ec3ab + name: Exome Seq Training Short W Cached Ref + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - variant-analysis + - galaxy-training-network + tools: + - gemini_inheritance + - gemini_load + - samtools_rmdup + - bcftools_norm + - snpEff + - samtool_filter2 + - freebayes + update_time: '2020-08-31' + versions: 0 +- create_time: '2020-05-03' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 1b3c4c9b1ab8032d + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1b3c4c9b1ab8032d + name: SNPs/EXONs for 02 different genes + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - tp_sort_header_tool + - gops_join_1 + - Grouping1 + - tp_head_tool + - comp1 + update_time: '2020-08-10' + versions: 0 +- create_time: '2020-06-28' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - SNP detection + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bcf230e526632064 + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=bcf230e526632064 + name: 'COVID-19: variation analysis on ARTIC PE data' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + tools: + - fastp + - vcfvcfintersect + - __UNZIP_COLLECTION__ + - ivar_trim + - multiqc + - tp_replace_in_line + - lofreq_call + - __ZIP_COLLECTION__ + - lofreq_indelqual + - qualimap_bamqc + - samtools_stats + - __FLATTEN__ + - lofreq_filter + - snpeff_sars_cov_2 + - samtools_view + - lofreq_viterbi + - ivar_removereads + - bwa_mem + update_time: '2020-06-28' + versions: 3 +- create_time: '2020-06-17' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - RNA-Seq analysis + - Transcriptome assembly + - Sequence composition calculation + - Sequence alignment + - Sequence annotation + - Sequencing quality control + edam_topic: [] + id: e045a6064ad5fdc4 + latest_version: 6 + license: null + link: https://usegalaxy.org.au/published/workflow?id=e045a6064ad5fdc4 + name: 'Workflow: Mapping uterine transcripts to human genome (h38) HISAT' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - CONVERTER_gz_to_uncompressed + - trimmomatic + - stringtie + - gffcompare + - deeptools_bam_coverage + - fastq_groomer + - hisat2 + update_time: '2020-06-25' + versions: 6 +- create_time: '2020-06-19' + creators: [] + doi: '' + edam_operation: + - Formatting + - Genome indexing + - Read mapping + - Validation + - Sequence contamination filtering + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: ccf936c5b2f2c2f3 + latest_version: 14 + license: null + link: https://usegalaxy.org.au/published/workflow?id=ccf936c5b2f2c2f3 + name: 'imported: COVID 19: Amplicon-ARTIC' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastp + - ivar_trim + - ivar_variants + - tp_sed_tool + - qualimap_bamqc + - ivar_consensus + - multiqc + - picard_MarkDuplicates + - samtool_filter2 + - bwa_mem + update_time: '2020-06-20' + versions: 14 +- create_time: '2020-06-19' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Sequence alignment analysis + - Genome indexing + - Sequence composition calculation + - Read mapping + - Variant calling + - Generation + - Sequence file editing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 1a159863e9d977a0 + latest_version: 5 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1a159863e9d977a0 + name: Workflow for Analysis of Genetic Variation + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - sam_merge2 + - vcfallelicprimitives + - snpSift_extractFields + - Remove beginning1 + - tp_sort_header_tool + - bamFilter + - picard_AddOrReplaceReadGroups + - vcffilter2 + - Grouping1 + - snpEff + - seqtk_trimfq + - picard_CleanSam + - picard_MarkDuplicates + - freebayes + - bwa_mem + update_time: '2020-06-19' + versions: 5 +- create_time: '2020-05-22' + creators: [] + doi: '' + edam_operation: + - Validation + - Sequence contamination filtering + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: fca05a51c9c91df4 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=fca05a51c9c91df4 + name: 'COVID 19: Amplicon-ARTIC' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - ARTIC + tools: + - fastp + - ivar_trim + - ivar_variants + - qualimap_bamqc + - ivar_consensus + - multiqc + - bwa_mem + update_time: '2020-05-25' + versions: 2 +- create_time: '2020-05-19' + creators: [] + doi: '' + edam_operation: + - Formatting + edam_topic: [] + id: 20d472fc5563a640 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640 + name: Visualise BIOM1 in Krona + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - cut_fr + - Remove beginning1 + - Cut1 + - bg_column_arrange_by_header + - biom_convert + - row_means + - krona-text + - Paste1 + - regex1 + update_time: '2020-05-19' + versions: 1 +- create_time: '2020-05-17' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 80a1493fb9593bb3 + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=80a1493fb9593bb3 + name: Ganesan_43828564_Bioinfo_Workshop1 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - cummeRbund + - Filter1 + update_time: '2020-05-18' + versions: 3 +- create_time: '2020-05-13' + creators: [] + doi: '' + edam_operation: + - Validation + - Statistical calculation + - Sequence composition calculation + - Sequencing quality control + edam_topic: [] + id: d3989c6c2c663cd3 + latest_version: 18 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d3989c6c2c663cd3 + name: noraml work flow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - cufflinks + - cuffdiff + - tophat2 + - fastq_quality_trimmer + - cuffmerge + - cummeRbund + - multiqc + update_time: '2020-05-15' + versions: 18 +- create_time: '2020-05-12' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 115896e8f4059e44 + latest_version: 11 + license: null + link: https://usegalaxy.org.au/published/workflow?id=115896e8f4059e44 + name: Workshop1_45074646 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - Filter1 + update_time: '2020-05-15' + versions: 11 +- create_time: '2020-05-14' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 73854e391eec51d0 + latest_version: 9 + license: null + link: https://usegalaxy.org.au/published/workflow?id=73854e391eec51d0 + name: Differential Gene Expression + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - 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transcriptomics + - galaxy-training-network + tools: + - scater_plot_dist_scatter + - scater_plot_pca + - scater_filter + - scater_create_qcmetric_ready_sce + update_time: '2020-04-22' + versions: 0 +- create_time: '2020-04-15' + creators: [] + doi: '' + edam_operation: + - Differential gene expression analysis + edam_topic: [] + id: 218ffb4438833bdd + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=218ffb4438833bdd + name: Clustering 3K PBMCs With Scanpy + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - transcriptomics + - galaxy-training-network + tools: + - anndata_manipulate + - scanpy_filter + - anndata_inspect + - Cut1 + - tp_cat + - scanpy_inspect + - scanpy_cluster_reduce_dimension + - scanpy_normalize + - tp_replace_in_column + - tp_tail_tool + - tp_awk_tool + - scanpy_plot + - scanpy_remove_confounders + - anndata_import + - Filter1 + update_time: '2020-04-22' + versions: 0 +- create_time: '2020-04-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 65a8ac91d6ded9a2 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=65a8ac91d6ded9a2 + name: Regression (from training material) + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - 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ml + - statistics + - galaxy-training-network + tools: + - plotly_ml_performance_plots + - sklearn_svm_classifier + update_time: '2020-04-09' + versions: 0 +- create_time: '2020-04-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: b0ee0c0a6a37f5ef + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b0ee0c0a6a37f5ef + name: Machine Learning + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - ml + - statistics + - galaxy-training-network + tools: + - sklearn_svm_classifier + update_time: '2020-04-09' + versions: 0 +- create_time: '2020-04-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 92b5a29a956a3afc + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=92b5a29a956a3afc + name: Age Prediction RNA-Seq + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - statistics + - galaxy-training-network + tools: + - sklearn_build_pipeline + - plotly_parallel_coordinates_plot + - sklearn_searchcv + update_time: '2020-04-09' + versions: 0 +- create_time: '2020-04-09' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 697945d5f9edbf39 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=697945d5f9edbf39 + name: Age Prediction DNA Methylation + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - statistics + - galaxy-training-network + tools: + - plotly_regression_performance_plots + - sklearn_build_pipeline + - sklearn_searchcv + - sklearn_ensemble + update_time: '2020-04-09' + versions: 0 +- create_time: '2020-04-07' + creators: [] + doi: '' + edam_operation: + - Sequence assembly + - Optimisation and refinement + - Genome assembly + edam_topic: [] + id: 8abcfe166f1a6cd8 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8 + name: Debruijn Graph + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + - galaxy-training-network + tools: + - fasta-stats + - spades + - velvetoptimiser + update_time: '2020-04-07' + versions: 1 +- create_time: '2020-04-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - De-novo assembly + - Sequence composition calculation + - Validation + - Visualisation + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: aee5b5645c51cac3 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=aee5b5645c51cac3 + name: Intro to Genome Assembly + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + - galaxy-training-network + tools: + - fastqc + - velvetg + - quast + - fastq_paired_end_interlacer + - multiqc + - velveth + update_time: '2020-04-07' + versions: 1 +- create_time: '2020-04-07' + creators: [] + doi: '' + edam_operation: + - Mapping + - Read mapping + - Sequence alignment + edam_topic: [] + id: b808cd1c0090b068 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068 + name: Ecoli Comparison + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + - galaxy-training-network + tools: + - collapse_dataset + - join1 + - fasta_compute_length + - tp_sort_header_tool + - datamash_ops + - random_lines1 + - mergeCols1 + - tp_grep_tool + - cat1 + - Grep1 + - tp_cat + - tp_sed_tool + - addValue + - lastz_wrapper_2 + - Filter1 + - fasta_filter_by_length + - Cut1 + - bedtools_complementbed + - bedtools_sortbed + - bedtools_intersectbed + update_time: '2020-04-07' + versions: 1 +- create_time: '2020-04-07' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Aggregation + - Coding region prediction + - Validation + - Genome annotation + - Visualisation + - Gene prediction + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: f01be6a7685ac476 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f01be6a7685ac476 + name: Unicycler training + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - assembly + - galaxy-training-network + tools: + - fastqc + - quast + - unicycler + - prokka + - multiqc + update_time: '2020-04-07' + versions: 1 +- create_time: '2020-04-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 8a20b3ed4a81263d + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8a20b3ed4a81263d + name: GROMACS Training Workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - computational-chemistry + - galaxy-training-network + tools: + - get_pdb + - gmx_sim + - gmx_solvate + - gmx_setup + - gmx_em + update_time: '2020-04-07' + versions: 1 +- create_time: '2020-04-07' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: c2f25a1bf07e8ab1 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=c2f25a1bf07e8ab1 + name: Simple Analysis + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - computational-chemistry + - galaxy-training-network + tools: + - bio3d_pca + - bio3d_rmsd + - bio3d_rmsf + update_time: '2020-04-07' + versions: 1 +- create_time: '2020-02-23' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Read mapping + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Generation + - Sequencing quality control + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: 557601292ea0f6f3 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=557601292ea0f6f3 + name: 'COVID-19: Alternate pre processing' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - Alternate-pre-processing + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - picard_MergeSamFiles + - minimap2 + - multiqc + - samtool_filter2 + - bwa_mem + update_time: '2020-02-23' + versions: 2 +- create_time: '2020-02-22' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Statistical calculation + - Sequence alignment analysis + - Local alignment + - Phylogenetic tree generation (from molecular sequences) + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: 42137e36791652bc + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=42137e36791652bc + name: 'COVID-19: RecSel' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - Recombination + tools: + - hyphy_gard + - rbc_mafft + - 'EMBOSS: tranalign100' + - hyphy_absrel + - fasttree + - 'EMBOSS: transeq101' + update_time: '2020-02-22' + versions: 0 +- create_time: '2020-02-22' + creators: [] + doi: '' + edam_operation: + - Sequence alignment analysis + - Local alignment + - Global alignment + - Sequence analysis + - Multiple sequence alignment + - Sequence alignment + edam_topic: [] + id: f21446cc44da50ce + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f21446cc44da50ce + name: 'COVID-19: S-gene AA' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - S-gene + tools: + - 'EMBOSS: tranalign100' + - 'EMBOSS: transeq101' + - rbc_mafft + update_time: '2020-02-22' + versions: 0 +- create_time: '2020-02-22' + creators: [] + doi: '' + edam_operation: + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 4cbc70a37a9da088 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=4cbc70a37a9da088 + name: 'COVID-19: Variation' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - Variation + tools: + - snpSift_extractFields + - collapse_dataset + - lofreq_call + - snpEff_build_gb + - snpEff + - lofreq_viterbi + - samtool_filter2 + - bwa_mem + update_time: '2020-02-22' + versions: 0 +- create_time: '2020-02-22' + creators: [] + doi: '' + edam_operation: + - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + - Multiple sequence alignment + - Formatting + - Phylogenetic tree generation (from molecular sequences) + edam_topic: [] + id: d62b6717202f42c9 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9 + name: 'COVID-19: MCRA' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - MCRA + tools: + - picard_NormalizeFasta + - Remove beginning1 + - Cut1 + - collapse_dataset + - ncbi_acc_download + - rbc_mafft + - fasttree + - tp_sed_tool + - Convert characters1 + update_time: '2020-02-22' + versions: 0 +- create_time: '2020-02-21' + creators: [] + doi: '' + edam_operation: + - Sequence assembly visualisation + - Aggregation + - Genome assembly + edam_topic: [] + id: 38d992baf9a2a2bc + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=38d992baf9a2a2bc + name: 'COVID-19: Assembly' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - Assembly + tools: + - bandage_image + - spades + - unicycler + - bandage_info + update_time: '2020-02-22' + versions: 0 +- create_time: '2020-02-21' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Data handling + - Genome indexing + - Sequence composition calculation + - Read mapping + - Pairwise sequence alignment + - Sequence contamination filtering + - Validation + - Box-Whisker plot plotting + - Generation + - Sequencing quality control + - Sequence alignment + - Scatter plot plotting + edam_topic: [] + id: bf80ef6e5f37deb7 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=bf80ef6e5f37deb7 + name: 'COVID-19: read pre-processing' + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - COVID-19 + - Pre-processing + tools: + - fastqc + - samtools_fastx + - nanoplot + - fastp + - picard_MergeSamFiles + - fasterq_dump + - minimap2 + - multiqc + - samtool_filter2 + - bwa_mem + update_time: '2020-02-22' + versions: 0 +- create_time: '2019-02-11' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Sequence composition calculation + - Coding region prediction + - Genome annotation + - Visualisation + - Gene prediction + - Sequence assembly validation + - Sequencing quality control + edam_topic: [] + id: 39c724282ee008e3 + latest_version: 13 + license: null + link: https://usegalaxy.org.au/published/workflow?id=39c724282ee008e3 + name: SIH_denovo_assembly_annotation + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - quast + - spades + - prokka + update_time: '2020-02-13' + versions: 13 +- create_time: '2019-10-30' + creators: [] + doi: '' + edam_operation: + - Peak detection + - Mass spectrum visualisation + - Chromatogram visualisation + - Validation + - Chromatographic alignment + - Filtering + - Label-free quantification + edam_topic: [] + id: f9e5caaf08a450ec + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=f9e5caaf08a450ec + name: LCMS Pre-Processing + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Metabolomics + - lcms + tools: + - xcms_merge + - abims_xcms_fillPeaks + - abims_xcms_retcor + - abims_xcms_group + - abims_CAMERA_annotateDiffreport + - abims_xcms_xcmsSet + - msnbase_readmsdata + - xcms_plot_chromatogram + update_time: '2019-10-30' + versions: 3 +- create_time: '2019-10-30' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 43109e341a5bd307 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=43109e341a5bd307 + name: LCMS-Data_Processing + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Metabolomics + - LCMS + tools: + - generic_filter + - wsdl_hmdb + - Univariate + - Batch_correction + - quality_metrics + update_time: '2019-10-30' + versions: 1 +- create_time: '2019-06-03' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: fa8d1de86aa944a2 + latest_version: 16 + license: null + link: https://usegalaxy.org.au/published/workflow?id=fa8d1de86aa944a2 + name: Galaxy Fungi Metagenomic Classification + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - mothur_summary_seqs + - mothur_make_group + - krona-text + - mothur_screen_seqs + - mothur_make_contigs + - mothur_count_seqs + - mothur_cluster_split + - mothur_merge_files + - mothur_make_shared + - mothur_unique_seqs + - mothur_align_seqs + - mothur_taxonomy_to_krona + - mothur_classify_otu + - mothur_classify_seqs + - mothur_pre_cluster + update_time: '2019-06-12' + versions: 16 +- create_time: '2018-08-13' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome assembly + - Phylogenetic tree generation + - Sequence composition calculation + - Optimisation and refinement + - Coding region prediction + - Phylogenetic tree visualisation + - Variant calling + - Genome annotation + - Gene prediction + - Sequence assembly + - Sequencing quality control + edam_topic: [] + id: fa76b66785ce38b8 + latest_version: 5 + license: null + link: https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8 + name: simon_pulsar_tester + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - velvet + - trimmomatic + - snippy + - shovill + - spades + - prokka + - velvetoptimiser + update_time: '2019-05-10' + versions: 5 +- create_time: '2019-05-07' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 1624a678c6791ca6 + latest_version: 12 + license: null + link: https://usegalaxy.org.au/published/workflow?id=1624a678c6791ca6 + name: group project 1 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + update_time: '2019-05-07' + versions: 12 +- create_time: '2019-04-03' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d42df3bb51a94a52 + latest_version: 6 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d42df3bb51a94a52 + name: BINF6000 - Workshop 1 - Workflow + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - Filter1 + update_time: '2019-04-05' + versions: 6 +- create_time: '2019-04-03' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: b518ee5540ed01fd + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=b518ee5540ed01fd + name: fatima + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - sort1 + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - fastq_trimmer + - Filter1 + update_time: '2019-04-04' + versions: 2 +- create_time: '2019-04-03' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: a3efc48b5992374e + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=a3efc48b5992374e + name: Workflow constructed from history 'abdulrahman' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - sort1 + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - fastq_trimmer + - Filter1 + update_time: '2019-04-04' + versions: 3 +- create_time: '2019-04-04' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d0933b5040adf902 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d0933b5040adf902 + name: Workflow constructed from history 'GROUP_AG_12' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - fastq_trimmer + update_time: '2019-04-04' + versions: 2 +- create_time: '2019-04-03' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: d1b604a5441dc4b0 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=d1b604a5441dc4b0 + name: Chenglong Workflow 'workshop1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - tp_sort_header_tool + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - fastq_trimmer + - Filter1 + update_time: '2019-04-04' + versions: 1 +- create_time: '2019-04-02' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 79572be1bf642251 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=79572be1bf642251 + name: Workflow constructed from history 'RNA analysis-19' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - fastq_trimmer + update_time: '2019-04-04' + versions: 2 +- create_time: '2019-04-03' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: ec202ccfb5f03d0d + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=ec202ccfb5f03d0d + name: final + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - Filter1 + update_time: '2019-04-03' + versions: 1 +- create_time: '2019-02-28' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Data handling + - Sequence composition calculation + - Primer removal + - Validation + - Sequence trimming + - Read pre-processing + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: bb0feff5d764df60 + latest_version: 4 + license: null + link: https://usegalaxy.org.au/published/workflow?id=bb0feff5d764df60 + name: Workflow constructed from history 'RNA-seq exercise' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - cutadapt + - rseqc_bam_stat + - rna_star + - multiqc + update_time: '2019-03-29' + versions: 4 +- create_time: '2018-11-26' + creators: [] + doi: '' + edam_operation: + - Formatting + edam_topic: [] + id: 4f837b7f90d5ebac + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac + name: Visualise BIOM1 in Krona + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - cut_fr + - Remove beginning1 + - Cut1 + - bg_column_arrange_by_header + - biom_convert + - row_means + - krona-text + - Paste1 + - regex1 + update_time: '2018-11-26' + versions: 1 +- create_time: '2018-11-08' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 177579096e009178 + latest_version: 7 + license: null + link: https://usegalaxy.org.au/published/workflow?id=177579096e009178 + name: Workflow constructed from history 'Completed-soil-metagenomics-analysis' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - mothur_summary_seqs + - mothur_make_group + - mothur_filter_seqs + - krona-text + - mothur_screen_seqs + - mothur_count_seqs + - mothur_cluster_split + - mothur_merge_files + - mothur_make_shared + - mothur_unique_seqs + - mothur_align_seqs + - mothur_taxonomy_to_krona + - mothur_classify_otu + - mothur_classify_seqs + - mothur_pre_cluster + update_time: '2018-11-09' + versions: 7 +- create_time: '2018-10-31' + creators: [] + doi: '' + edam_operation: + - Sequence read processing + - Phylogenetic analysis + - Taxonomic classification + - Visualisation + - Sequence clustering + - DNA barcoding + - Sequencing quality control + edam_topic: [] + id: 57fe85f947217994 + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=57fe85f947217994 + name: Workflow-GTN-Metagenomics-Soil-Tutorial + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - mothur_summary_seqs + - mothur_make_group + - mothur_filter_seqs + - krona-text + - mothur_screen_seqs + - mothur_count_seqs + - mothur_cluster_split + - mothur_merge_files + - mothur_make_shared + - mothur_unique_seqs + - mothur_align_seqs + - mothur_taxonomy_to_krona + - mothur_classify_otu + - mothur_classify_seqs + - mothur_pre_cluster + update_time: '2018-11-07' + versions: 3 +- create_time: '2018-10-15' + creators: [] + doi: '' + edam_operation: + - Genome visualisation + - Genome indexing + - Generation + - Read mapping + - Sequence alignment + edam_topic: [] + id: 8031655d71b59d15 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=8031655d71b59d15 + name: Oct 18 Workflow constructed from history 'Copy of 'Published-RNA-seq-bacteria'' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - rgdifferentialcount + - jbrowse + - htseqsams2mxlocal + - fml_gtf2gff + - bwa_mem + update_time: '2018-10-15' + versions: 1 +- create_time: '2018-09-03' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Genome visualisation + - Genome assembly + - Sequence composition calculation + - Coding region prediction + - Genome annotation + - Antimicrobial resistance prediction + - Gene prediction + - Sequencing quality control + - Multilocus sequence typing + edam_topic: [] + id: 914330feb75ea9ab + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab + name: trim_assemble_annotate_180903 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - abricate + - trimmomatic + - spades + - mlst + - fasta-stats + - prokka + - jbrowse + update_time: '2018-09-03' + versions: 2 +- create_time: '2018-07-24' + creators: [] + doi: '' + edam_operation: + - Genome annotation + - Genome visualisation + - Genome assembly + - Gene prediction + - Coding region prediction + edam_topic: [] + id: 87cdeb05b1ebeab0 + latest_version: 3 + license: null + link: https://usegalaxy.org.au/published/workflow?id=87cdeb05b1ebeab0 + name: Reads to Annotation + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - prokka + - spades + - jbrowse + update_time: '2018-07-24' + versions: 3 +- create_time: '2018-06-19' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 59e8d2bbbae020b1 + latest_version: 2 + license: null + link: https://usegalaxy.org.au/published/workflow?id=59e8d2bbbae020b1 + name: CutColumns + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - Cut1 + update_time: '2018-06-19' + versions: 2 +- create_time: '2018-03-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 9beae9b0c863d335 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=9beae9b0c863d335 + name: BINF6000 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - Filter1 + update_time: '2018-03-28' + versions: 0 +- create_time: '2018-03-28' + creators: [] + doi: '' + edam_operation: [] + edam_topic: [] + id: 89531196e32e330e + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=89531196e32e330e + name: BINF6000-18 + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - Filter1 + update_time: '2018-03-28' + versions: 0 +- create_time: '2017-06-09' + creators: [] + doi: '' + edam_operation: + - Statistical calculation + - Formatting + - Genome indexing + - Sequence composition calculation + - Mapping + - Read mapping + - Variant calling + - Generation + - Sequence alignment + - Sequencing quality control + edam_topic: [] + id: 3d5deed70ac9bde4 + latest_version: 9 + license: null + link: https://usegalaxy.org.au/published/workflow?id=3d5deed70ac9bde4 + name: "Copy of 'Annotation of data obtained after the sequencing of gastrointestinal\ + \ cancer samples (processed following the TruSeq\xAE Custom Amplicon Low Input\ + \ Library Prep protocol) using MiSeq or NextSeq illumina sequencing'" + number_of_steps: null + source: https://usegalaxy.org.au + tags: + - Annotation + - NextSeq + - MiSeq + - Illumina + tools: + - fastqc + - trimmomatic + - gatk2_indel_realigner + - gatk_indel_realigner + - samtools_sort + - bam_to_sam + - picard_AddOrReplaceReadGroups + - gatk2_unified_genotyper + - vcftools_isec + - bedtools_intersectbed + - gatk2_realigner_target_creator + - snpEff + - gatk_realigner_target_creator + - bowtie2 + - freebayes + - bwa_mem + update_time: '2017-07-14' + versions: 9 +- create_time: '2017-03-27' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 60c5675ed2f4a7d8 + latest_version: 1 + license: null + link: https://usegalaxy.org.au/published/workflow?id=60c5675ed2f4a7d8 + name: Workflow constructed from history 'Workshop1_5' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - fastq_groomer + update_time: '2017-05-18' + versions: 1 +- create_time: '2017-03-30' + creators: [] + doi: '' + edam_operation: + - Sequence composition calculation + - Statistical calculation + - Sequencing quality control + edam_topic: [] + id: 39bb22274ede7500 + latest_version: 0 + license: null + link: https://usegalaxy.org.au/published/workflow?id=39bb22274ede7500 + name: Workflow from 'Workshop 1' + number_of_steps: null + source: https://usegalaxy.org.au + tags: [] + tools: + - fastqc + - sort1 + - trimmomatic + - cufflinks + - cuffdiff + - tophat2 + - cuffmerge + - fastq_groomer + - Filter1 + update_time: '2017-03-30' + versions: 0 diff --git a/docs/_includes/index.html b/docs/_includes/index.html new file mode 100644 index 00000000..7a792a6d --- /dev/null +++ b/docs/_includes/index.html @@ -0,0 +1,28140 @@ + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ExpandGalaxy wrapper idGalaxy wrapper versionConda versionConda idStatusbio.tool idbio.tool nameEDAM operationEDAM topicDescriptionbio.tool descriptionbiiiStatusSourceToolShed categoriesToolShed idGalaxy wrapper ownerGalaxy wrapper source
askor0.23.58.1bioconductor-limmaTo updateAskoR links EdgeR and AskOmicsTo updatehttps://github.com/askomics/askoRTranscriptomicsaskor_degenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/askor
baric_archive1.1.0To updateA data source tool to fetch data from a BARIC Archive server.To updatehttps://www.cesgo.org/catibaric/Data Sourcegenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive
braker2.1.6To updateBRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .To updatehttps://github.com/Gaius-Augustus/BRAKERGenome annotationbrakergenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/braker
braker33.0.8To updateBRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .To updatehttps://github.com/Gaius-Augustus/BRAKERGenome annotationbraker3genouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/braker
feelnc2asko0.11.7.8perl-bioperlTo updateConvert FeelNC GTF to GFF3To updatehttps://github.com/tderrien/FEELncConvert Formatsfeelnc2askogenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko
gcms2isocor0.1.0openjdkTo updateConversion from GCMS PostRun Analysis to IsocorTo updateMetabolomicsgcms2isocorgenouest
get_pairs0.3pythonTo updateSeparate paired and unpaired reads from two fastq filesTo updateFastq Manipulationget_pairsgenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs
helixer0.3.2To updateGene calling with Deep Neural NetworksTo updatehttps://github.com/weberlab-hhu/HelixerGenome annotationhelixergenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/helixer
logol1.7.81.7.8logolUp-to-dateLogol is a pattern matching grammar language and a set of tools to search a pattern in a sequenceUp-to-datehttp://logol.genouest.org/web/app.php/logolSequence Analysisgenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/logol
meneco1.5.21.5.2menecoUp-to-dateMeneco computes minimal completions to your draft network with reactions from a repair networkUp-to-datehttp://bioasp.github.io/meneco/Systems Biologymenecogenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/meneco
miranda2asko0.2perlTo updateConverts miRanda output into AskOmics formatTo updateConvert Formatsmiranda2askogenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko
openlabcds2csv0.1.0openjdkTo updateCreates a summary of several "Internal Standard Report" OpenLabCDS results.To updateMetabolomicsopenlabcds2csvgenouest
peptimapper2.0To updateProteogenomics workflow for the expert annotation of eukaryotic genomesTo updatehttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9Proteomicsgenouest
Ensembl-REST0.1.2requestsTo updateA suite of Galaxy tools designed to work with Ensembl REST API.To updatehttps://rest.ensembl.orgData Sourceearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST
GAFA0.3.1To updateGene Align and Family AggregatorTo updatehttp://aequatus.tgac.ac.ukVisualizationgafaearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/
TreeBest1.9.2.post01.9.2.post1treebestTo updateTreeBeST bestTo updatehttp://treesoft.sourceforge.net/treebest.shtmlPhylogeneticstreebest_bestearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest
apoc1.0+galaxy11b16apocTo updateLarge-scale structural comparison of protein pocketsTo updatehttp://cssb.biology.gatech.edu/APocComputational chemistryapocearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/
blast_parser0.1.2To updateConvert 12- or 24-column BLAST output into 3-column hcluster_sg inputTo updatehttps://github.com/TGAC/earlham-galaxytools/Phylogeneticsblast_parserearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser
ete3.1.23.1.1ete3To updateAnalyse phylogenetic trees using the ETE ToolkitTo updatehttp://etetoolkit.org/Phylogeneticseteearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete
export_to_cluster0.0.2EXPORT_DIR_PREFIXTo updateExport datasets to clusterTo updatehttps://github.com/TGAC/earlham-galaxytools/Data Exportexport_to_clusterearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/
gblocks0.91b0.91bgblocksUp-to-dateGblocksUp-to-datehttp://molevol.cmima.csic.es/castresana/Gblocks.htmlSequence Analysisgblocksearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks
gstf_preparation0.4.3pythonTo updateGeneSeqToFamily preparation converts data for the workflowTo updatehttps://github.com/TGAC/earlham-galaxytools/Convert Formatsgstf_preparationearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation
hcluster_sg0.5.1.10.5.1hcluster_sgTo updateHierarchically clustering on a sparse graphTo updatehttps://github.com/douglasgscofield/hclusterPhylogeneticshcluster_sgearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg
hcluster_sg_parser0.2.1To updateConverts hcluster_sg 3-column output into lists of idsTo updatehttps://github.com/TGAC/earlham-galaxytools/Phylogeneticshcluster_sg_parserearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser
lotus22.322.32lotus2Up-to-datelotus2lotus2Sequence feature detectionMetagenomicsLotuS2 OTU processing pipelineLotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.Up-to-datehttp://lotus2.earlham.ac.uk/Metagenomicslotus2earlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
miranda3.3a+galaxy13.3amirandaTo updateFinds potential target sites for miRNAs in genomic sequencesTo updatehttp://www.microrna.org/RNAmirandaearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda
plotheatmap1.01.64.0bioconductor-preprocesscoreTo updateThis tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.To updateComputational chemistryplotheatmapearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap
rdock1.02013.1rDockTo updateDocking ligands to proteins and nucleic acidsTo updatehttp://rdock.sourceforge.net/Computational chemistryrdockearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/
replace_chromosome_names0.1pythonTo updateReplace chromosome namesTo updateText Manipulationreplace_chromosome_namesearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/
rsat_filter_snps0.1To updateFilter SNPs in RSAT Matrix Scan outputTo updatehttps://github.com/TGAC/earlham-galaxytools/ChIP-seq, Systems Biologyrsat_filter_snpsearlhamhttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps
smart_domains0.1.01.7.8perl-bioperlTo updateSMART domainsTo updatehttp://smart.embl.de/Sequence Analysissmart_domainsearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains
smina1.02017.11.9sminaTo updatesmina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimizationTo updatehttps://sourceforge.net/projects/smina/Computational chemistrysminaearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/
t_coffee13.45.0.484626413.46.0.919e8c6bt-coffeeTo updateT-CoffeeTo updatehttp://www.tcoffee.org/Sequence Analysist_coffeeearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee
abacas1.13.23mummerTo updateOrder and Orientate ContigsTo updatehttps://github.com/phac-nml/abacasAssemblyabacasnmlhttps://github.com/phac-nml/abacas
assemblystats1.1.01.7.8perl-bioperlTo updateSummarise an assembly (e.g. N50 metrics)To updatehttps://github.com/phac-nml/galaxy_toolsAssemblyassemblystatsnmlhttps://github.com/phac-nml/galaxy_tools
bam2mappingstats1.1.0perlTo updateGenerates mapping stats from a bam file.To updatehttps://github.com/phac-nml/galaxy_toolsAssemblybam2mappingstatsnmlhttps://github.com/phac-nml/galaxy_tools
bamclipper1.0.01.0.0bamclipperUp-to-dateSoft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.Up-to-datehttps://github.com/tommyau/bamclipperSequence Analysisbamclippernmlhttps://github.com/tommyau/bamclipper
biohansel2.4.02.6.1bio_hanselTo updateHeidelberg and Enteritidis SNP ElucidationTo updatehttps://github.com/phac-nml/biohanselSequence Analysisbiohanselnmlhttps://github.com/phac-nml/biohansel
biohansel_bionumeric_converter0.2.0pandasTo updateConvert BioHansel output data to a Bionumerics friendly formTo updatehttps://github.com/phac-nml/galaxy_toolsText Manipulationbiohansel_bionumeric_converternml
bundle_collections1.3.02.54perl-getopt-longTo updateTool to bundle up list collection into a single zip to be downloadTo updateSequence Analysisbundle_collectionsnml
collapse_collection5.1.0gawkTo updateCollection tool that collapses a list of files into a single datasset in order of appears in collectionTo updateSequence Analysiscollapse_collectionsnml
combineJSON0.1To updateJSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.To updateSequence Analysiscombine_jsonnml
combine_assembly_stats1.02.54perl-getopt-longTo updateCombine multiple Assemblystats datasets into a single tabular reportTo updatehttps://github.com/phac-nml/galaxy_toolsAssemblycombine_assemblystatsnmlhttps://github.com/phac-nml/galaxy_tools
combine_tabular_collection0.1To updateCombine Tabular Collection into a single fileTo updateSequence Analysiscombine_tabular_collectionnml
concat_paired0.2To updateConcatenate paired datasetsTo updatehttps://github.com/phac-nml/concatText Manipulationconcat_pairednmlhttps://github.com/phac-nml/concat
cryptogenotyper1.01.0cryptogenotyperUp-to-dateCryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers.Up-to-datehttps://github.com/phac-nml/CryptoGenotyperSequence Analysiscryptogenotypernmlhttps://github.com/phac-nml/CryptoGenotyper
csvtk0.20.00.29.0csvtkTo updateRapid data investigation and manipulation of csv/tsv filesTo updatehttps://bioinf.shenwei.me/csvtk/Text Manipulationcsvtknmlhttps://github.com/shenwei356/csvtk
ectyper1.0.01.0.0ectyperUp-to-dateEC-Typer - in silico serotyping of Escherichia coli speciesUp-to-datehttps://github.com/phac-nml/ecoli_serotypingSequence Analysisectypernmlhttps://github.com/phac-nml/ecoli_serotyping
fasta2bed1.0.01.7.8perl-bioperlTo updateConvert multiple fasta file into tabular bed file formatTo updatehttps://github.com/phac-nml/galaxy_toolsSequence Analysisfasta2bednmlhttps://github.com/phac-nml/galaxy_tools
fasta_extract1.1.01.7.8perl-bioperlTo updateextract single fasta from multiple fasta fileTo updatehttps://toolshed.g2.bx.psu.edu/view/nml/fasta_extractSequence Analysisfasta_extractnmlhttps://toolshed.g2.bx.psu.edu/view/nml/fasta_extract
fastqc_stats1.21.7.8perl-bioperlTo updateSummary multiple FastQC into a single tabular line reportTo updatehttps://github.com/phac-nml/galaxy_toolsSequence Analysisfastqc_statsnmlhttps://github.com/phac-nml/galaxy_tools
feht0.1.01.1.0fehtTo updateAutomatically identify makers predictive of groups.To updatehttps://github.com/phac-nml/galaxy_toolsSequence Analysisfehtnmlhttps://github.com/phac-nml/galaxy_tools
filter_spades_repeats1.0.11.7.8perl-bioperlTo updateRemove short and repeat contigs/scaffoldsTo updatehttps://github.com/phac-nml/galaxy_tools/Assemblyfilter_spades_repeatsnmlhttps://github.com/phac-nml/galaxy_tools/
getmlst0.1.4.10.2.0srst2To updateDownload MLST datasets by species from pubmlst.orgTo updateSequence Analysisgetmlstnml
gnali1.1.01.1.0gnaliUp-to-dateA tool to find nonessential, loss-of-function gene variantsUp-to-datehttps://github.com/phac-nml/gnali/Variant Analysisgnalinmlhttps://github.com/phac-nml/gnali/
hivtrace1.0.11.5.0hivtraceTo updateAn application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.To updateSequence Analysishivtracenmlhttps://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace
kaptive0.3.02.0.6kaptiveTo updateKaptive reports information about capsular (K) loci found in genome assemblies.To updateSequence Analysiskaptivenml
kat_filter2.32.4.2katTo updateFiltering kmers or reads from a database of kmers hashesTo updateSequence Analysiskat_filternml
kat_sect2.32.4.2katTo updateSEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.To updatekat_sectnml
mauve_contig_mover1.0.102.4.0.r4736mauveTo updateOrder a draft genome relative to a related reference genomeTo updatehttps://github.com/phac-nml/mauve_contig_moverSequence Analysismauve_contig_movernmlhttps://github.com/phac-nml/mauve_contig_mover
mob_suite3.0.33.1.8mob_suiteTo updateMOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assembliesTo updatehttps://github.com/phac-nml/mob-suiteSequence Analysismob_suitenmlhttps://github.com/phac-nml/mob-suite
mrbayes1.0.23.2.7mrbayesTo updateA program for the Bayesian estimation of phylogeny.To updateSequence Analysismrbayesnml
mykrobe_parser0.1.4.1r-baseTo updateRScript to parse the results of mykrobe predictor.To updatehttps://github.com/phac-nml/mykrobe-parserSequence Analysismykrobe_parsernmlhttps://github.com/phac-nml/mykrobe-parser
pangolin1.1.144.3pangolinTo updatePhylogenetic Assignment of Named Global Outbreak LINeagesTo updatehttps://github.com/hCoV-2019/pangolinSequence Analysispangolinnmlhttps://github.com/hCoV-2019/pangolin
patrist0.1.2pythonTo updateExtract Patristic Distance From a TreeTo updatehttps://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02Phylogeneticspatristnmlhttps://github.com/phac-nml/patrist
plasmid_profiler0.1.6rTo updateExplores plasmid content in WGS dataTo updateplasmid_profilernml
plasmid_profiler_suiteTo updatePlasmid Profiler suite defining all dependencies for Plasmid ProfilerTo updateSequence Analysissuite_plasmid_profilernml
plasmidspades1.13.15.5spadesTo updateGenome assembler for assemblying plasmidTo updateAssemblyplasmidspadesnml
pneumocat1.2.11.2.1pneumocatUp-to-datePneumococcal Capsular Typing of illumina fastq readsUp-to-datehttps://github.com/phe-bioinformatics/PneumoCaTVariant Analysispneumocatnmlhttps://github.com/phe-bioinformatics/PneumoCaT
promer1.2pythonTo updateAligns two sets of contigs and reports amino acid substitutions between themTo updatehttps://github.com/phac-nml/promerAssemblypromernmlhttps://github.com/phac-nml/promer
pseudogenome1.0.01.7.8perl-bioperlTo updateCreate a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.To updatehttps://github.com/phac-nml/galaxy_toolsSequence Analysispseudogenomenml
quasitools0.7.00.7.0quasitoolsUp-to-dateA collection of tools for analysing Viral QuasispeciesUp-to-datehttps://github.com/phac-nml/quasitoolsSequence Analysisquasitoolsnmlhttps://github.com/phac-nml/quasitools
refseq_masher0.1.20.1.2refseq_masherUp-to-dateFind what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.Up-to-datehttps://github.com/phac-nml/refseq_masherSequence Analysisrefseq_mashernmlhttps://github.com/phac-nml/refseq_masher
seqtk_nml1.0.11.4seqtkTo updateTool to downsample fastq readsTo updatehttps://github.com/lh3/seqtkSequence Analysisseqtk_nmlnmlhttps://github.com/phac-nml/snvphyl-galaxy
sistr_cmd1.1.11.1.1sistr_cmdUp-to-dateSISTR in silico serotyping toolUp-to-datehttps://github.com/phac-nml/sistr_cmdSequence Analysissistr_cmdnml
smalt0.7.60.7.6smaltUp-to-dateSMALT aligns DNA sequencing reads with a reference genome.Up-to-datehttp://www.sanger.ac.uk/science/tools/smalt-0Sequence Analysissmaltnmlhttps://sourceforge.net/projects/smalt/
spades_header_fixer1.1.2+galaxy1sedTo updateFixes Spades Fasta idsTo updatehttps://github.com/phac-nml/galaxy_toolsFasta Manipulationspades_fasta_header_fixernmlhttps://github.com/phac-nml/galaxy_tools
spatyper0.3.30.3.3spatyperUp-to-dateDetermines SPA type based on repeats in a submitted staphylococcal protein A fasta file.Up-to-datehttps://github.com/HCGB-IGTP/spaTyperSequence Analysisspatypernmlhttps://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper
spolpred1.0.1spolpredTo updateA program for predicting the spoligotype from raw sequence readsTo updateSequence Analysisspolprednml
srst20.3.70.2.0srst2To updateShort Read Sequence Typing for Bacterial PathogensTo updateSequence Analysissrst2nml
staramr0.10.00.10.0staramrUp-to-dateScan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.Up-to-datehttps://github.com/phac-nml/staramrSequence Analysisstaramrnmlhttps://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr
stringmlst1.1.00.6.3stringMLSTTo updateRapid and accurate identification of the sequence type (ST)To updateSequence Analysisstringmlstnml
tree_relabeler1.1.01.7.8perl-bioperlTo updateRelabels the tips of a newick formatted tree.To updateText Manipulationtree_relabelernmlhttps://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler
wade0.2.5+galaxy10.2.6wadeTo updateidentify regions of interestTo updatehttps://github.com/phac-nml/wadeSequence Analysiswadenmlhttps://github.com/phac-nml/wade
camera1.48.00.4_1r-snowTo updateTo updateMetabolomicscameraworkflow4metabolomics
correlation_analysis1.0.1+galaxy01.1_4r-batchTo update[Metabolomics][W4M] Metabolites Correlation AnalysisTo updatehttp://workflow4metabolomics.orgMetabolomicscorrelation_analysisworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/
genformr8genformTo updategenform: generation of molecular formulas by high-resolution MS and MS/MS dataTo updatehttps://sourceforge.net/projects/genform/Metabolomicsgenformworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/
influx_data_manager1.0.01.0.0influx-si-data-managerUp-to-dateHandling influx_si data inputs in Galaxy workflowsUp-to-datehttps://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/Metabolomicsinflux_si_data_managerworkflow4metabolomicshttps://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager
influx_si7.0.17.0.2influx_siTo updatemetabolic flux estimation based on [in]stationary labelingTo updatehttps://github.com/sgsokol/influxMetabolomicsinflux_siworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/
ipo1.10.01.28.0bioconductor-ipoTo update[W4M][LC-MS] IPOTo updatehttps://github.com/rietho/IPOMetabolomicsipolecorguillehttps://github.com/rietho/IPO
isoplot1.3.0+galaxy11.3.1isoplotTo updateIsoplot is a software for the visualisation of MS data from C13 labelling experimentsTo updateMetabolomics, Visualizationisoplotworkflow4metabolomicshttps://github.com/llegregam/Isoplot/tree/main
kmd_hmdb_data_plot1.0.0pythonTo updateretrieves data from KMD HMDB API and produce plot and csv fileTo updatehttps://github.com/workflow4metabolomics/tools-metabolomicsMetabolomicskmd_hmdb_data_plotworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/
mixmodel4repeated_measures3.1.0r-lme4To update[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed modelTo updatehttp://workflow4metabolomics.orgMetabolomicsmixmodel4repeated_measuresworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics
ms2snoop2.2.1r-baseTo update[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.To updatehttp://workflow4metabolomics.orgMetabolomicsms2snoopworkflow4metabolomics
nmr_annotation3.0.01.1_4r-batchTo update[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimationTo updatehttp://workflow4metabolomics.orgMetabolomicsnmr_annotationmarie-tremblay-metatoulhttps://github.com/workflow4metabolomics/nmr_annotation
nmr_annotation2d2.0.01.1_4r-batchTo update[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectraTo updatehttp://workflow4metabolomics.orgMetabolomics2dnmrannotationmarie-tremblay-metatoulhttps://github.com/workflow4metabolomics/tools-metabolomics
nmr_preprocessing1.1_4r-batchTo update[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correctionTo updatehttp://workflow4metabolomics.orgMetabolomicsnmr_preprocessingmarie-tremblay-metatoulhttps://github.com/workflow4metabolomics/nmr_preprocessing
normalization1.0.71.1_4r-batchTo update[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed dataTo updatehttp://workflow4metabolomics.orgMetabolomicsnormalizationmarie-tremblay-metatoulhttps://github.com/workflow4metabolomics/normalization
physiofit3.3.23.3.2physiofitUp-to-datePhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxesUp-to-datephysiofit.readthedocs.ioMetabolomicsphysiofitworkflow4metabolomicshttps://github.com/MetaSys-LISBP/PhysioFit
physiofit_manager1.0.11.0.1physiofit_data_managerUp-to-dateHandling of physiofit input filesUp-to-datehttps://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_ManagerMetabolomicsphysiofit_managerworkflow4metabolomics
xcms3.12.04.0.0bioconductor-xcmsTo updateTo updatehttps://github.com/sneumann/xcmsMetabolomicsxcmsworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/
apollo4.2.13apolloTo updateAccess an Apollo instance from GalaxyTo updatehttps://github.com/galaxy-genome-annotation/python-apolloWeb Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo
askomics0.5askocliTo updateGalaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/To updatehttps://github.com/askomics/Web Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics
chado2.3.9python-chadoTo updateGalaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chadoTo updatehttps://github.com/galaxy-genome-annotation/python-chadoWeb Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado
genenotebook0.4.130.4.13genobooUp-to-dateGalaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.ioUp-to-datehttps://genenotebook.github.ioWeb Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook
jbrowsepythonTo updateA tool allowing to export a JBrowse dataset into a JBrowse docker containerTo updatehttps://jbrowse.orgWeb Servicesjbrowse_to_containerggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse
repeatexplorer22.3.8To updateTool for annotation of repeats from unassembled shotgun reads.To updatehttps://github.com/repeatexplorer/repex_tareanGenome annotationrepeatexplorer2ggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2
tripal3.2.1python-tripalTo updateGalaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripalTo updatehttps://github.com/galaxy-genome-annotation/python-tripalWeb Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal
w4mcorcov0.98.18r-baseTo updateOPLS-DA Contrasts of Univariate ResultsTo updatehttps://github.com/HegemanLab/w4mcorcov_galaxy_wrapperMetabolomicsw4mcorcoveschen42https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master
w4mclassfilter0.98.19r-baseTo updateFilter W4M data by values or metadataTo updatehttps://github.com/HegemanLab/w4mclassfilter_galaxy_wrapperMetabolomicsw4mclassfiltereschen42https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master
w4mjoinpn0.98.28.25coreutilsTo updateJoin positive- and negative-mode W4M datasetsTo updatehttps://github.com/HegemanLab/w4mjoinpn_galaxy_wrapperMetabolomicsw4mjoinpneschen42https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master
2d_auto_threshold0.0.5-2scikit-imageTo updatescikit-imagescikit-imageImage analysis, Image annotation, Visualisation, Data handlingImaging, Software engineering, Literature and languageAutomatic thresholdingScikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.scikit-imageTo updatehttps://github.com/bmcvImaging2d_auto_thresholdimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/
2d_feature_extraction0.1.1-2pandasTo updatescikit-imagescikit-imageImage analysis, Image annotation, Visualisation, Data handlingImaging, Software engineering, Literature and language2D feature extractionScikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.scikit-imageTo updatehttps://github.com/bmcvImaging2d_feature_extractionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/
2d_filter_segmentation_by_features0.0.1-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, Bioinformaticsfilter segmentation by rulesDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImaging2d_filter_segmentation_by_featuresimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/
2d_histogram_equalization0.0.1-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, Bioinformatics2d histogram equalizationDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImaging2d_histogram_equalizationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/
2d_simple_filter0.0.3-3scikit-imageTo updatescikit-imagescikit-imageImage analysis, Image annotation, Visualisation, Data handlingImaging, Software engineering, Literature and language2d simple filterScikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.scikit-imageTo updatehttps://github.com/bmcvImaging2d_simple_filterimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/
3d_tensor_feature_dimension_reduction0.0.1numpyTo updateDimensionality reduction for features (channels) of 3D tensor data using UMAPTo updatehttps://github.com/BMCV/galaxy-image-analysisImaging3d_tensor_feature_dimension_reductionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/
anisotropic_diffusion0.2-2scikit-imageTo updateAnisotropic image diffusionTo updatehttps://github.com/bmcvImaginganisotropic_diffusionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/
bfconvert6.7.0+galaxy26.7.0bftoolsTo updateConvert imagepython-bioformatsTo updatehttps://github.com/bmcvImaging, Convert Formatsbfconvertimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/
binary2labelimage0.5scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsBinary 2 label imageDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingbinary2labelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/
binaryimage2points0.1-2numpyTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsBinary Image to PointsDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingbinaryimage2pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/
bioformats2raw0.7.0To updateConvert image to OME-ZarrTo updatehttps://github.com/Euro-BioImagingImaging, Convert Formatsbioformats2rawimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw
color-deconvolution0.8-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsColor-deconvolution methodsDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingcolor_deconvolutionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/
concat_channels0.2-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsConcatenate imagesDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingconcat_channelsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/
coordinates_of_roi0.0.4-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsCoordinates of ROIDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingcoordinates_of_roiimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/
count_objects0.0.5-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsCount ObjectsDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingcount_objectsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/
curl_post0.0.2curlTo updateSend file via cURL POSTTo updatehttps://github.com/bmcvData Export, Web Servicescurl_postimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post
curve_fitting0.0.3-2numpyTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsPolynomial curve fitting to data pointsDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/BMCV/galaxy-image-analysisImagingcurve_fittingimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/
detection_viz0.3-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsDetection VisualizationDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingdetection_vizimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/
image_info5.7.16.7.0bftoolsTo updateExtracts image metadatapython-bioformatsTo updatehttps://github.com/bmcvImagingimage_infoimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/
image_registration_affine0.0.3-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsIntensity-based Image RegistrationDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingimage_registration_affineimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/
imagecoordinates_flipaxis0.1-2pandasTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsFlip coordinate axesDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingimagecoordinates_flipaxisimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/
labelimage2points0.2-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsLabel Image to PointsDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImaginglabelimage2pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/
landmark_registration0.1.0-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsLandmark RegistrationDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImaginglandmark_registrationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/
mahotas-features0.7-2mahotasTo updateCompute image features using mahotas.mahotas-feature-computationTo updatehttps://github.com/luispedro/mahotasImagingmahotas_featuresimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/
mergeneighboursinlabelimage0.3-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsMerge Neighbours in Label ImageDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingmergeneighboursinlabelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage
overlay_images0.0.4scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsOverlay two imagesDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/BMCV/galaxy-image-analysisImagingoverlay_imagesimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/
permutate_axis0.2-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsPermutates axesDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingpermutate_axisimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/
points2binaryimage0.2-1scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsPoints to Binary ImageDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingpoints2binaryimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/
points2labelimage0.3-2numpyTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsPoints to label imageDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingpoints2labelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/
points_association_nn0.0.3-2numpyTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsAssociation of points in consecutive framesDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/BMCV/galaxy-image-analysisImagingpoints_association_nnimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/
projective_transformation0.1.2-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsProjective transformationDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingprojective_transformationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/
projective_transformation_points0.1.1-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsProjective transformation of ROIs defined by pixel (point) coordinatesDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingprojective_transformation_pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/
rfove2023.11.12To updaterfoveRFOVEImage analysisCell biology, Biomedical science, ImagingPerform segmentation region-based fitting of overlapping ellipsesRFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.To updatehttps://sites.google.com/site/costaspanagiotakis/research/csImagingrfoveimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/
scale_image0.4-2pillowTo updatescikit-imagescikit-imageImage analysis, Image annotation, Visualisation, Data handlingImaging, Software engineering, Literature and languageScale imageScikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.scikit-imageTo updatehttps://github.com/bmcvImagingscale_imageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/
segmetrics1.41.4.1segmetricsTo updatesegmetricsSegMetricsImage analysisImage segmentation and object detection performance measuresImage segmentation and object detection performance measuressegmetricsTo updatehttps://github.com/bmcvImagingsegmetricsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/
slice_image0.3-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsSlice imageDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingslice_imageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/
split_labelmap0.2-2scikit-imageTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsSplit LabelmapsDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingsplit_labelmapimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/
spot_detection_2d0.0.3-2imageioTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsSpot detection in 2D image sequenceDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/BMCV/galaxy-image-analysisImagingspot_detection_2dimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/
superdsm0.2.00.2.0superdsmUp-to-datesuperdsmSuperDSMImage analysisGlobally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy imagesSuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.superdsmUp-to-datehttps://github.com/bmcvImagingsuperdsmimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/
unzip6.0unzipTo updateUnzip fileTo updatehttps://github.com/bmcvConvert Formatsunzipimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/
visceral-evaluatesegmentation0.5-22015.07.03visceral-evaluatesegmentationTo updateVisceral Project - Evaluate Segmentation Toolevaluatesegmentation-toolTo updatehttps://github.com/bmcvImagingvisceral_evaluatesegmentationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation
wsi_extract_top_view0.2-2scikit-imageTo updateWSI Extract Top ViewTo updatehttps://github.com/bmcvImagingwsi_extract_top_viewimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/
add_value1.0.1perlTo updateAdd a value as a new column.To updateText Manipulationadd_valuedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value
annotation_profiler1.0.00.11.0bx-pythonTo updateProfile Annotations for a set of genomic intervalsTo updateGenomic Interval Operationsannotation_profilerdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler
best_regression_subsets1.0.0numpyTo updatePerform Best-subsets RegressionTo updateSequence Analysis, Variant Analysisbest_regression_subsetsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets
blat_coverage_report1.0.0To updatePolymorphism of the ReadsTo updateNext Gen Mappers, Sequence Analysisblat_coverage_reportdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report
blat_mapping1.0.0To updateCoverage of the Reads in wiggle formatTo updateNext Gen Mappers, Sequence Analysisblat_mappingdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping
bowtie_wrappers1.2.01.3.1bowtieTo updateGalaxy wrappers for the Bowtie short read mapping tools.To updatehttp://bowtie-bio.sourceforge.net/Next Gen Mappersbowtie_wrappersdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers
canonical_correlation_analysis1.0.0RTo updateCanonical Correlation AnalysisTo updateStatisticscanonical_correlation_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis
categorize_elements_satisfying_criteria1.0.0To updateCategorize Elements satisfying criteria.To updateStatisticscategorize_elements_satisfying_criteriadevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria
ccat0.0.23.0ccatTo updateControl-based ChIP-seq Analysis ToolTo updateChIP-seqccatdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat
cd_hit_dup0.0.14.8.1cd-hit-auxtoolsTo updatesimple tool for removing duplicates from sequencing readsTo updateMetagenomics, Sequence Analysiscd_hit_dupdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup
change_case1.0.1perlTo updateConvert column case.To updateText Manipulationchange_casedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case
compute_motif_frequencies_for_all_motifs1.0.0To updateCompute Motif Frequencies For All Motifs, motif by motif.To updateSequence Analysis, Statisticscompute_motif_frequencies_for_all_motifsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs
compute_motifs_frequency1.0.0To updateCompute Motif Frequencies in indel flanking regions.To updateSequence Analysis, Statisticscompute_motifs_frequencydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency
compute_q_values1.0.1RTo updateCompute q-values based on multiple simultaneous tests p-valuesTo updateStatisticscompute_q_valuesdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values
condense_characters1.0.0To updateCondense consecutive characters.To updateText Manipulationcondense_charactersdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters
convert_characters1.0.1pythonTo updateConvert delimiters to tab.To updateText Manipulationconvert_charactersdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters
convert_solid_color2nuc1.0.0To updateConvert Color Space to NucleotidesTo updateFasta Manipulationconvert_solid_color2nucdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc
correlation1.0.0rpyTo updateCorrelation for numeric columnsTo updateStatisticscorrelationdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation
count_gff_features0.21.1.0galaxy-opsTo updateCount GFF FeaturesTo updateSequence Analysiscount_gff_featuresdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features
ctd_batch1.0.0To updateCTD analysis of chemicals, diseases, or genesTo updateSequence Analysisctd_batchdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch
cummerbund2.16.0fonts-conda-ecosystemTo updateWrapper for the Bioconductor cummeRbund libraryTo updatehttps://bioconductor.org/packages/release/bioc/html/cummeRbund.htmlRNA, Visualizationcummerbunddevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund
cummerbund_to_tabular1.0.1To updateRegenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.To updateConvert Formats, Next Gen Mapperscummerbund_to_tabulardevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular
cut_columns1.0.2To updateSelect columns from a dataset.To updateText Manipulationcut_columnsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns
delete_overlapping_indels1.0.0To updateDelete Overlapping Indels from a chromosome indels fileTo updateSequence Analysisdelete_overlapping_indelsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels
dgidb_annotator0.1To updateAnnotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)To updateSystems Biology, Variant Analysisdgidb_annotatordevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator
divide_pg_snp1.0.0To updateSeparate pgSnp alleles into columnsTo updateSequence Analysisdivide_pg_snpdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp
draw_stacked_barplots1.0.0RTo updateDraw Stacked Bar Plots for different categories and different criteriaTo updateGraphics, Statisticsdraw_stacked_barplotsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots
dwt_cor_ava_perclass1.0.11.7.5r-waveslimTo updateCompute P-values and Correlation Coefficients for Feature OccurrencesTo updateStatisticsdwt_cor_ava_perclassdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass
dwt_cor_avb_all1.0.11.7.5r-waveslimTo updateCompute P-values and Correlation Coefficients for Occurrences of Two Set of FeaturesTo updateStatisticsdwt_cor_avb_alldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all
dwt_ivc_all1.0.11.7.5r-waveslimTo updateCompute P-values and Second Moments for Feature OccurrencesTo updateStatisticsdwt_ivc_alldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all
dwt_var_perclass1.0.11.7.5r-waveslimTo updateCompute P-values and Max Variances for Feature OccurrencesTo updateStatisticsdwt_var_perclassdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass
dwt_var_perfeature1.0.2r-bitopsTo updateWavelet variance using Discrete Wavelet TransfomsTo updateStatisticsdwt_var_perfeaturedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature
express1.1.11.5.1eXpressTo updateQuantify the abundances of a set of target sequences from sampled subsequencesTo updateRNAexpressdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/express
fasta_compute_length1.0.3pythonTo updateCompute sequence lengthTo updateFasta Manipulationfasta_compute_lengthdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length
fasta_concatenate_by_species0.0.10.11.0bx-pythonTo updateConcatenate FASTA alignment by speciesTo updateFasta Manipulationfasta_concatenate_by_speciesdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species
fasta_filter_by_length1.2pythonTo updateFilter sequences by lengthTo updateFasta Manipulationfasta_filter_by_lengthdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length
fasta_to_tabular1.1.1pythonTo updateFASTA-to-Tabular converterTo updateFasta Manipulationfasta_to_tabulardevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular
fastq_trimmer_by_quality1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ Quality Trimmer by sliding windowUp-to-dateFastq Manipulationfastq_trimmer_by_qualitydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality
fastqsolexa_to_fasta_qual1.0.0To updateFASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA dataTo updateConvert Formats, Fastq Manipulationfastqsolexa_to_fasta_qualdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual
featurecounter2.0.00.11.0bx-pythonTo updateFeature coverageTo updateSequence Analysis, Variant Analysisfeaturecounterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter
filter_transcripts_via_tracking0.1To updateFilter Combined TranscriptsTo updateRNAfilter_transcripts_via_trackingdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking
generate_pc_lda_matrix1.0.0To updateGenerate a Matrix for using PC and LDATo updateSequence Analysisgenerate_pc_lda_matrixdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix
getindelrates_3way1.0.00.11.0bx-pythonTo updateEstimate Indel Rates for 3-way alignmentsTo updateSequence Analysis, Variant Analysisgetindelrates_3waydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way
getindels_2way1.0.0numpyTo updateFetch Indels from pairwise alignmentsTo updateSequence Analysis, Variant Analysisgetindels_2waydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way
gmaj2.0.1To updateGMAJ Multiple Alignment ViewerTo updateVisualizationgmajdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj
hisat1.0.3hisatTo updateHISAT is a fast and sensitive spliced alignment program.To updatehttp://ccb.jhu.edu/software/hisat/index.shtmlAssemblyhisatdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat
histogram1.0.42.7.8rpy2To updateHistogram of a numeric columnTo updateGraphics, Statisticshistogramdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram
indels_3way1.0.3To updateFetch Indels from 3-way alignmentsTo updateSequence Analysisindels_3waydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way
kernel_canonical_correlation_analysis1.0.0rpyTo updateKernel Canonical Correlation AnalysisTo updateStatisticskernel_canonical_correlation_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis
kernel_principal_component_analysis1.0.0rpyTo updateKernel Principal Component AnalysisTo updateStatisticskernel_principal_component_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis
lastz_paired_reads1.1.11.04.22lastzTo updateGalaxy wrapper for the Lastz alignment tool on paired readsTo updateNext Gen Mapperslastz_paired_readsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads
lda_analysis1.0.1RTo updatePerform Linear Discriminant AnalysisTo updateGraphics, Statisticslda_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis
linear_regression1.0.1RTo updatePerform Linear RegressionTo updateStatisticslinear_regressiondevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression
logistic_regression_vif1.0.1numpyTo updatePerform Logistic Regression with vifTo updateSequence Analysis, Variant Analysis, Statisticslogistic_regression_vifdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif
maf_cpg_filter1.0.00.11.0bx-pythonTo updateMask CpG/non-CpG sites from MAF fileTo updateSequence Analysis, Variant Analysismaf_cpg_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter
mapping_to_ucsc1.0.0To updateFormat mapping data as UCSC custom trackTo updateVisualization, Convert Formats, Next Gen Mappersmapping_to_ucscdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc
megablast_xml_parser1.0.1pythonTo updateParse blast XML outputTo updateNext Gen Mappers, Convert Formatsmegablast_xml_parserdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser
merge_cols1.0.3pythonTo updateMerge columns together.To updateText Manipulationmerge_colsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols
microsatellite_birthdeath1.0.0To updateIdentify microsatellite births and deathsTo updateSequence Analysismicrosatellite_birthdeathdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath
microsats_alignment_level1.0.0sputnikTo updateExtract Orthologous Microsatellites from pair-wise alignmentsTo updateSequence Analysis, Variant Analysismicrosats_alignment_leveldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level
microsats_mutability1.1.00.11.0bx-pythonTo updateEstimate microsatellite mutability by specified attributesTo updateSequence Analysis, Variant Analysismicrosats_mutabilitydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability
mine0.0.1MINETo updateMaximal Information-based Nonparametric ExplorationTo updateVariant Analysisminedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/mine
multispecies_orthologous_microsats1.0.0bx-sputnikTo updateExtract orthologous microsatellitesTo updateSequence Analysis, Variant Analysismultispecies_orthologous_microsatsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats
mutate_snp_codon1.0.0To updateMutate Codons with SNPsTo updateVariant Analysismutate_snp_codondevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon
partialr_square1.0.0RTo updateCompute partial R squareTo updateStatisticspartialr_squaredevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square
pearson_correlation1.0.0To updatePearson and apos Correlation between any two numeric columnsTo updateStatisticspearson_correlationdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation
pgsnp2gd_snp1.0.0To updateConvert from pgSnp to gd_snpTo updateVariant Analysispgsnp2gd_snpdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp
pileup_interval1.0.30.11.0bx-pythonTo updatePileup-to-Interval condenses pileup format into ranges of basesTo updateSAMpileup_intervaldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval
pileup_parser1.0.2perlTo updateFilter pileup on coverage and SNPsTo updatehttps://github.com/galaxyproject/tools-devteam/SAMpileup_parserdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser
plot_from_lda1.0.1RTo updateDraw ROC plot on "Perform LDA" outputTo updateGraphics, Statisticsplot_from_ldadevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda
principal_component_analysis1.0.2rpyTo updatePrincipal Component AnalysisTo updateStatisticsprincipal_component_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis
quality_filter1.0.10.11.0bx-pythonTo updateFilter nucleotides based on quality scoresTo updateSequence Analysis, Variant Analysisquality_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter
rcve1.0.0RTo updateCompute RCVETo updateSequence Analysis, Variant Analysisrcvedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve
remove_beginning1.0.0To updateRemove lines from the beginning of a file.To updateText Manipulationremove_beginningdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning
rmap1.0.02.1rmapTo updateRMAP for Solexa Short Reads AlignmentTo updateNext Gen Mappersrmapdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap
rmapq1.0.02.1rmapTo updateRMAPQ for Solexa Short Reads Alignment with Quality ScoresTo updateNext Gen Mappersrmapqdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq
sam2interval1.0.2pythonTo updateConvert SAM to interval.To updateSAMsam2intervaldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval
sam_bitwise_flag_filter1.0.1pythonTo updateFilter SAM on bitwise flag valuesTo updateSAMsam_bitwise_flag_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter
scatterplot1.0.3numpyTo updateScatterplot of two numeric columnsTo updateGraphics, Statisticsscatterplotdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot
short_reads_figure_high_quality_length1.0.0rpyTo updateHistogram of high quality score readsTo updateSequence Analysis, Graphicsshort_reads_figure_high_quality_lengthdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length
short_reads_figure_score1.0.2fontconfigTo updateBuild base quality distributionTo updateSequence Analysis, Graphicsshort_reads_figure_scoredevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score
short_reads_trim_seq1.0.0To updateSelect high quality segmentsTo updateFastq Manipulationshort_reads_trim_seqdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq
show_beginning1.0.0To updateSelect lines from the beginning of a file.To updateText Manipulationshow_beginningdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning
show_tail1.0.0To updateSelect lines from the end of a file.To updateText Manipulationshow_taildevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail
sicer1.11.1SICERUp-to-dateStatistical approach for the Identification of ChIP-Enriched RegionsUp-to-datehttps://home.gwu.edu/~wpeng/Software.htmChIP-seqsicerdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer
split_paired_reads1.0.0To updateSplit paired end readsTo updateFastq Manipulationsplit_paired_readsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads
substitution_rates1.0.0To updateEstimate substitution rates for non-coding regionsTo updateSequence Analysis, Variant Analysissubstitution_ratesdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates
substitutions1.0.10.11.0bx-pythonTo updateFetch substitutions from pairwise alignmentsTo updateSequence Analysis, Variant Analysissubstitutionsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions
t_test_two_samples1.0.1RTo updateT Test for Two SamplesTo updateStatisticst_test_two_samplesdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples
table_annovar0.2annovarTo updateAnnotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filteredTo updateVariant Analysistable_annovardevteamNonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar
tabular_to_fasta1.1.1pythonTo updateTabular-to-FASTATo updateConvert Formatstabular_to_fastadevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta
tophat1.5.01.19.2samtoolsTo updateTophat for IlluminaTo updateRNA, Next Gen Mapperstophatdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat
tophat22.1.12.5.3bowtie2To updateTophat - fast splice junction mapper for RNA-Seq readsTo updatehttp://ccb.jhu.edu/software/tophat/index.shtmlRNA, Next Gen Mapperstophat2devteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2
tophat_fusion_post0.1blast+To updateWrapper for Tophat-Fusion post stepTo updateTranscriptomicstophat_fusion_postdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post
trimmer0.0.1To updateTrim leading or trailing characters.To updateText Manipulationtrimmerdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer
ucsc_custom_track1.0.1pythonTo updateBuild custom track for UCSC genome browserTo updateSequence Analysisucsc_custom_trackdevteamhttps://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track
varscan_version_22.4.22.4.6varscanTo updateVarScan wrapperTo updatehttps://dkoboldt.github.io/varscan/Variant Analysisvarscan_version_2devteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2
vcf2pgsnp1.0.0To updateVCF to pgSnpTo updateVariant Analysisvcf2pgsnpdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp
vcf_annotate1.0.0To updateAnnotate a VCF file (dbSNP, hapmap)To updateVariant Analysisvcf_annotatedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate
vcf_extract1.0.0To updateExtract reads from a specified regionTo updateVariant Analysisvcf_extractdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract
vcf_filter1.0.0To updateFilter a VCF fileTo updateVariant Analysisvcf_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter
vcf_intersect1.0.0To updateGenerate the intersection of two VCF filesTo updateVariant Analysisvcf_intersectdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect
weightedaverage1.0.11.1.0galaxy-opsTo updateAssign weighted-average of the values of features overlapping an intervalTo updateSequence Analysis, Variant Analysisweightedaveragedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage
windowsplitter1.0.10.11.0bx-pythonTo updateMake windowsTo updateSequence Analysis, Variant Analysiswindowsplitterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter
xy_plot1.0.2r-baseTo updatePlotting tool for multiple series and graph typesTo updateGraphics, Statisticsxy_plotdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot
basecoverage1.0.00.11.0bx-pythonTo updateBase Coverage of all intervalsTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsbasecoveragedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage
cluster1.0.00.11.0bx-pythonTo updateCluster the intervals of a datasetTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsclusterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster
complement1.0.00.11.0bx-pythonTo updateComplement intervals of a datasetTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationscomplementdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement
concat1.0.10.11.0bx-pythonTo updateConcatenate two bed filesTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsconcatdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat
coverage1.0.00.11.0bx-pythonTo updateCoverage of a set of intervals on second set of intervalsTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationscoveragedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage
flanking_features4.0.10.11.0bx-pythonTo updateFetch closest non-overlapping feature for every intervalTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsflanking_featuresdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features
get_flanks1.0.00.11.0bx-pythonTo updateGet flanks returns flanking region/s for every geneTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsget_flanksdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks
intersect1.0.00.11.0bx-pythonTo updateIntersect the intervals of two datasetsTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsintersectdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect
join1.0.00.11.0bx-pythonTo updateJoin the intervals of two datasets side-by-sideTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsjoindevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join
merge1.0.00.11.0bx-pythonTo updateMerge the overlapping intervals of a datasetTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsmergedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge
subtract1.0.00.11.0bx-pythonTo updateSubtract the intervals of two datasetsTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationssubtractdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract
subtract_query0.10.11.0bx-pythonTo updateSubtract Whole Dataset from another datasetTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationssubtract_querydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query
tables_arithmetic_operations1.0.0perlTo updateArithmetic Operations on tablesTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationstables_arithmetic_operationsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations
hgv_fundo1.0.0To updateFunDO human genes associated with disease termsTo updateSequence Analysishgv_fundodevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo
hgv_hilbertvis1.0.0RTo updateHVIS visualization of genomic data with the Hilbert curveTo updatehttps://www.ebi.ac.uk/huber-srv/hilbert/Graphics, Visualizationhgv_hilbertvisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis
snpfreq1.0.1RTo updatesnpFreq significant SNPs in case-control dataTo updateVariant Analysis, Statisticssnpfreqdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq
find_diag_hits1.0.00.10.0taxonomyTo updateFind diagnostic hitsTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicsfind_diag_hitsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits
gi2taxonomy1.1.10.10.0taxonomyTo updateFetch taxonomic representationTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicsgi2taxonomydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy
kraken2tax1.2+galaxy0gawkTo updateConvert Kraken output to Galaxy taxonomy data.To updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicskraken2taxdevteamhttps://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/
lca_wrapper1.0.10.10.0taxonomyTo updateFind lowest diagnostic rankTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicslca_wrapperdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper
poisson2test1.0.00.10.0taxonomyTo updatePoisson two-sample testTo updatehttps://bitbucket.org/natefoo/taxonomyStatistics, Metagenomicspoisson2testdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test
t2ps1.0.00.10.0taxonomyTo updateDraw phylogenyTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicst2psdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps
t2t_report1.0.00.10.0taxonomyTo updateSummarize taxonomyTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicst2t_reportdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report
vcftools_annotate0.1echoTo updateAnnotate VCF using custom/user-defined annotationsTo updatehttps://vcftools.github.io/Variant Analysisvcftools_annotatedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate
vcftools_compare0.11.11tabixTo updateCompare VCF files to get overlap and uniqueness statisticsTo updatehttps://vcftools.github.io/Variant Analysisvcftools_comparedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare
vcftools_consensus0.1.111.19.2samtoolsTo updateApply VCF variants to a fasta file to create consensus sequenceTo updatehttps://vcftools.github.io/Variant Analysisvcftools_consensusdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus
vcftools_isec0.1.11.11tabixTo updateIntersect multiple VCF datasetsTo updatehttps://vcftools.github.io/Variant Analysisvcftools_isecdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec
vcftools_merge0.1.111.11tabixTo updateMerge multiple VCF datasets into a single datasetTo updatehttps://vcftools.github.io/Variant Analysisvcftools_mergedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge
vcftools_slice0.1echoTo updateSubset VCF dataset by genomic regionsTo updatehttps://vcftools.github.io/Variant Analysisvcftools_slicedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice
vcftools_subset0.11.11tabixTo updateSelect samples from a VCF datasetTo updatehttps://vcftools.github.io/Variant Analysisvcftools_subsetdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset
10x_bamtofastq1.4.11.4.110x_bamtofastqUp-to-dateConverts 10x Genomics BAM to FASTQUp-to-datehttps://github.com/10XGenomics/bamtofastqConvert Formats10x_bamtofastqbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq
AggregateAlignments0.6.00.6.0graphclust-wrappersUp-to-dateAggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.Up-to-dateRNAgraphclust_aggregate_alignmentsrnateamhttps://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments
AlignCluster0.10.6.0graphclust-wrappersTo updateAlign predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.To updateRNAgraphclust_align_clusterrnateamhttps://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster
CMFinder0.40.6.0graphclust-wrappersTo updateDetermines consensus motives for sequences.To updateRNAgraphclust_cmfinderrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder
CollectResults0.50.6.0graphclust-wrappersTo updatePost-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.To updateRNAgraphclust_postprocessingrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults
CollectResultsNoAlign0.50.6.0graphclust-wrappersTo updateRedundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.To updateRNAgraphclust_postprocessing_no_alignrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign
GSPAN0.40.6.0graphclust-wrappersTo updateSecond step of GraphClustTo updateRNAgraphclust_fasta_to_gspanrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN
LocARNAGraphClust0.40.6.0graphclust-wrappersTo updateMLocARNA computes a multiple sequence-structure alignment of RNA sequences.To updateRNAgraphclust_mlocarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust
NSPDK9.2.3.10.6.0graphclust-wrappersTo updateProduces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.To updateRNAgraphclust_nspdkrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK
Plotting0.4seabornTo updatePlotting results for GraphClustTo updateRNAgraphclust_motif_finder_plotrnateamhttps://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting
PrepareForMlocarna0.40.6.0graphclust-wrappersTo updateThis tool prepares files for locarna step.To updateRNAgraphclust_prepocessing_for_mlocarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna
Preprocessing0.50.6.0graphclust-wrappersTo updatePreprocessing input for GraphClustTo updateRNAgraphclust_preprocessingrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust
Structure_GSPAN0.40.6.0graphclust-wrappersTo updateConvert RNA structure to GSPAN graphsTo updateRNAstructure_to_gspanrnateamhttps://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN
agat1.2.01.3.0agatTo updateagatAGATData handling, Genome annotationGenomicsGTF/GFF analysis toolkitAnother Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.To updatehttps://github.com/NBISweden/AGATConvert Formats, Statistics, Fasta Manipulationagatbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/agat
antismash6.1.17.1.0antismashTo updateantismashantiSMASHSequence clustering, Gene prediction, Differential gene expression analysisMolecular interactions, pathways and networks, Gene and protein familiesAntismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clustersRapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.To updatehttps://antismash.secondarymetabolites.orgSequence Analysisantismashbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash
atactk_trim_adapters0.1.60.1.9atactkTo updateTrim adapters from paired-end HTS reads.To updatehttps://github.com/ParkerLab/atactk/Fastq Manipulationatactk_trim_adaptersrnateamhttps://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters
augustus3.1.03.5.0augustusTo updateAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.To updatehttp://bioinf.uni-greifswald.de/augustus/Sequence Analysisaugustusbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/augustus
bamhash1.11.1bamhashUp-to-dateHash BAM and FASTQ files to verify data integrityUp-to-datehttps://github.com/DecodeGenetics/BamHashSequence Analysisbamhashbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/bamhash
barcode_collapse0.1.00.22.0pysamTo updatePaired End randomer aware duplicate removal algorithmTo updatehttps://github.com/YeoLab/gscriptsRNA, Sequence Analysisbarcode_collapsernateamhttps://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse
bigwig_to_bedgraph0.1.0ucsc_toolsTo updateConvert from bigWig to bedGraph formatTo updateConvert Formatsbigwig_to_bedgraphbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph
biomodelsML1To updateRandom Forest model to predict efficacy of immune checkpoint blockade across multiple cancer patient cohortsTo updatehttps://www.ebi.ac.uk/biomodels/BIOMD0000001066Machine Learningbiomodels_biomd0000001066bgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML
bionano3.7.0To updateBionano Solve is a set of tools for analyzing Bionano dataTo updatehttps://bionanogenomics.com/Assemblybionanobgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/bionano
bismark0.22.10.24.2bismarkTo updateA tool to map bisulfite converted sequence reads and determine cytosine methylation statesTo updatehttps://www.bioinformatics.babraham.ac.uk/projects/bismark/Sequence Analysis, Next Gen Mappersbismarkbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/bismark
blobtoolkit4.0.7To updateIdentification and isolation non-target data in draft and publicly available genome assemblies.To updatehttps://blobtoolkit.genomehubs.org/Sequence Analysis, Assemblyblobtoolkitbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit
blockbuster0.1.20.0.1.1blockbusterTo updateBlockbuster detects blocks of overlapping reads using a gaussian-distribution approach.To updatehttp://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.htmlRNA, Sequence Analysisblockbusterrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/blockbuster
canu2.22.2canuUp-to-datecanuCANUDe-novo assemblyGenomicsCanu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.Up-to-datehttps://github.com/marbl/canucanubgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/canu
cellpose3.0.1To updateCellpose is an anatomical segmentation algorithmTo updatehttps://github.com/MouseLand/cellposeImagingcellposebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/cellpose
cellprofilerTo updateCellProfilerCellProfilerQuantification, Image analysis, ParsingImaging, Microarray experiment, Genotype and phenotypecellProfiler wrapperTool for quantifying data from biological images, particularly in high-throughput experiments.cellprofilerTo updateImagingcellprofilerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools
cellprofiler_v44.2.6To updatecellProfiler4 wrapperTo updateImagingcellprofiler4bgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools
chipseeker1.32.01.38.0bioconductor-chipseekerTo updateA tool for ChIP peak annotation and visualizationTo updatehttps://bioconductor.org/packages/release/bioc/html/ChIPseeker.htmlChIP-seq, Genome annotationchipseekerrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/chipseeker
circexplorer1.1.9.01.1.10circexplorerTo updateA combined strategy to identify circular RNAs (circRNAs and ciRNAs)To updatehttps://github.com/YangLab/CIRCexplorerSequence Analysis, RNAcircexplorerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/circexplorer
combine_metaphlan_humann0.3.0pythonTo updatecombine_metaphlan_and_humannCombine Metaphlan and HUMAnNAggregationMetagenomics, Molecular interactions, pathways and networksCombine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances"This tool combine MetaPhlAn outputs and HUMANnN outputs." - Galaxy tool wrapperTo updateMetagenomicscombine_metaphlan2_humann2bebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2
compare_humann2_output0.2.0To updatecompare_humann2_outputsCompare HUMAnN2 outputsComparisonMetagenomics, Gene and protein familiesCompare outputs of HUMAnN2 for several samples and extract similar and specific information"This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples." - Galaxy tool wrapperTo updateMetagenomicscompare_humann2_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
cpat3.0.53.0.5cpatUp-to-dateCoding-potential assessment tool using an alignment-free logistic regression model.Up-to-datehttps://github.com/liguowang/cpatTranscriptomicscpatbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/cpat
crt1.2.01.2crisper_recognition_toolTo updateCRISPR Recognition ToolTo updateSequence Analysiscrispr_recognition_toolbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/crt
diff3.7diffutilsTo updateGNU diff tool that calculates the differences between two files.To updatehttp://www.gnu.org/software/diffutils/Text Manipulationdiffbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/diff
diffbindTo updateDiffbind provides functions for processing ChIP-Seq data.To updatehttp://bioconductor.org/packages/release/bioc/html/DiffBind.htmlChIP-seqdiffbindbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/diffbind
edta2.2.0edtaTo updateedtaThe Extensive de novo TE Annotator (EDTA)De-novo assembly, Deisotoping, Genome annotationWorkflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organismsThe EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations.The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.To updatehttps://github.com/oushujun/EDTAVariant Analysisedtabgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/edta
epicseg@VERSION_STRING@1.0epicsegTo updateEpiCSeg is a tool for conducting chromatin segmentation.To updatehttps://github.com/lamortenera/epicsegEpigeneticsepicsegrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/epicseg
fastq_info0.25.10.25.2fastq_utilsTo updateFASTQ info allows to validate single or paired fastq filesTo updatehttps://github.com/nunofonseca/fastq_utilsFastq Manipulationfastq_infobgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/fastq_info
file_manipulation0.4pythonTo updateThis tool returns all unique lines from a tab-separated file.To updatehttps://github.com/bgruening/galaxytools/tree/master/tools/file_manipulationText Manipulationuniquebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation
find_subsequences0.31.70biopythonTo updateTo updatefind_subsequencesbgruening
flye2.9.32.9.3flyeUp-to-dateAssembly of long and error-prone reads.Up-to-datehttps://github.com/fenderglass/Flye/Assemblyflyebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/flye
footprint1.0.01.0.1footprintTo updateFind transcription factor footprintsTo updatehttps://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/Epigeneticsfootprintrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/footprint
format_cd_hit_output1.0.0+galaxy1To updateFormat CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping fileTo updateFasta Manipulationformat_cd_hit_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/
format_metaphlan2_output0.2.0To updateformat_metaphlan2_outputFormat metaphlan2 outputFormattingTaxonomy, MetagenomicsFormat MetaPhlAn2 output to extract abundance at different taxonomic levels"This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)." - Galaxy tool wrapperTo updateMetagenomicsformat_metaphlan2_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/
gfastats1.3.61.3.6gfastatsUp-to-dategfastatsgfastatsData handlingComputational biologyTool for generating sequence statistics and simultaneous genome assembly file manipulation.gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.Up-to-datehttps://github.com/vgl-hub/gfastatsSequence Analysisgfastatsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/gfastats
glimmer_hmmTo updateGlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)To updatehttps://ccb.jhu.edu/software/glimmerhmm/Sequence Analysisglimmer_hmmbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm
gotohscan1.3.01.3gotohscanTo updateFind subsequences in dbTo updateSequence Analysisgotohscanrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/gotohscan
graph_converter0.1.0To updateConvert between different graph formatsTo updateConvert Formatsgraph_converterbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/graph_converter
graphclust0.1GraphClustTo updateGraphClust can be used for structural clustering of RNA sequences.To updatehttp://www.bioinf.uni-freiburg.de/Software/GraphClust/RNAgraphclustbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/graphclust
graphmap0.5.20.6.3graphmapTo updateMapper for long, error-prone reads.To updatehttps://github.com/isovic/graphmap/Assemblygraphmapbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/graphmap
hclust20.991.0.0hclust2To updatePlots heatmapsTo updatehttps://bitbucket.org/nsegata/hclust2/Data Visualizationhclust2rnateamhttps://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2
hictk0.0.80.0.9hictkTo updatehictk, a blazing-fast toolkit to work with .hic and .cool filesTo updatehttps://github.com/paulsengroup/hictkhictkbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/hictk
hicup0.9.2To updateThe HiCUP-Pipeline from the Bioinformatics Babraham Institute.To updatehttps://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.htmlEpigeneticshicupbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/hicup
hifiasm0.19.80.19.8hifiasmUp-to-dateA fast haplotype-resolved de novo assemblerUp-to-datehttps://github.com/chhylp123/hifiasmAssemblyhifiasmbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/hifiasm
homerTo updateSoftware for motif discovery and next generation sequencing analysis.To updatehttp://homer.salk.edu/homer/Sequence Analysishomerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/homer
illumina_methylation_analyser0.1RscriptTo updateMethylation analyzer for Illumina 450k DNA emthylation microarraysTo updatehttps://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyserSequence Analysisillumina_methylation_analyserbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser
bia-ftplinks0.1.0wgetTo updateTool to query ftp links for study from bioimage archiveTo updateImagingbia_downloadbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools
graphicsmagick1.3.421.3.26graphicsmagickTo updateContains tools based on GraphicsMagickTo updatehttp://www.graphicsmagick.orgImaginggraphicsmagickbgrueninghttps://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/
imagej2To updateimagejImageJ2Image analysis, Image annotation, VisualisationImagingImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.imagej2To updatehttp://fiji.scImagingimagej2imgteamhttps://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2
woundhealing1.6.11.6.1fiji-morpholibjUp-to-dateTool to automate quantification of wound healing in high-throughput microscopy scratch assaysUp-to-datehttps://git.embl.de/grp-cba/wound-healing-htm-screenImagingWound healing scratch assay image analysisbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools
instagraal0.1.6To updateinstagraalinstaGRAALGenome assembly, Mapping assembly, Genetic mapping, ScaffoldingSequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sitesLarge genome reassembly based on Hi-C dataChromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)To updatehttps://github.com/koszullab/instaGRAALAssemblyinstagraalbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/instagraal
iprscan5To updateInterproscan queries the interpro database and provides annotations.To updatehttp://www.ebi.ac.uk/Tools/pfa/iprscan5/Sequence Analysisiprscan5bgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/iprscan5
itsx1.1.31.1.3itsxUp-to-dateITSxITSxSequence feature detectionFunctional, regulatory and non-coding RNA, MicrobiologyITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.Up-to-datehttps://microbiology.se/software/itsx/Metagenomicsitsxbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/itsx
jupyter_job0.0.1To updateRun jupyter notebook script in GalaxyTo updateMachine Learningrun_jupyter_jobbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job
labels1.0.5.0labelsTo updateremaps and annotates alignmentsTo updatehttps://github.com/bgruening/galaxytools/tree/master/tools/labelsSequence Analysislabelsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/labels
lighter1.01.1.2lighterTo updateLighter is a kmer-based error correction method for whole genome sequencing dataTo updateSequence Analysis, Fasta Manipulationlighterbgrueninghttps://github.com/mourisl/Lighter
mafft7.5087.520mafftTo updateMAFFTMAFFTMultiple sequence alignmentSequence analysisMultiple alignment program for amino acid or nucleotide sequencesMAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.To updateRNAmafftrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/mafft
mavedb0.9To updatedata source for MaveDBTo updateData Sourcemavedb_importerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/
mcl14.13722.282mclTo updateMarkov Cluster AlgorithmTo updatehttp://micans.org/mcl/Sequence Analysis, Metagenomicsmclbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/mcl
methtools0.1.1methtoolsTo updatetools for methylation analysisTo updatehttps://github.com/bgruening/galaxytools/tree/master/tools/methtoolsSequence Analysismethtoolsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/methtools
methyldackel0.5.20.6.1methyldackelTo updateA tool for processing bisulfite sequencing alignmentsTo updatehttps://github.com/dpryan79/MethylDackelSequence Analysispileomethbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/methyldackel
methylkit0.99.21.28.0bioconductor-methylkitTo updateA method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.To updatehttp://bioconductor.org/packages/release/bioc/html/methylKit.htmlEpigeneticsmethylkitrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/methylkit
metilene0.2.6.10.2.8metileneTo updateDifferential DNA methylation callingTo updateRNA, Statisticsmetilenernateamhttps://github.com/bgruening/galaxytools/tree/master/tools/metilene
miclip1.2.0RscriptTo updateIdentification of binding sites in CLIP-Seq data.To updatehttps://cran.r-project.org/src/contrib/Archive/MiClip/Sequence Analysismiclipbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/miclip
minced0.2.00.4.2mincedTo updateMinCED - Mining CRISPRs in Environmental DatasetsTo updatehttp://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_READMESequence Analysismincedbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/minced
minipolish0.1.30.1.3minipolishUp-to-dateminipolishminipolishLocalised reassembly, Read depth analysisSequence assembly, SequencingPolishing miniasm assembliesA tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.Up-to-datehttps://github.com/rrwick/MinipolishSequence Analysisminipolishbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/minipolish
mitohifi3To updateAssembly mitogenomes from Pacbio HiFi read.To updatehttps://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2Assemblymitohifibgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/mitohifi
molecule2gspan0.22.3.90dev7d621d9openbabelTo updateconverterTo updatehttps://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspanConvert Formatsmolecule_to_gspanbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan
music_deconvolution0.1.10.1.1music-deconvolutionUp-to-dateMulti-subject Single Cell deconvolution (MuSiC)Up-to-datehttps://github.com/xuranw/MuSiCTranscriptomicsmusicbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/music/
nanopolish0.14.00.14.0nanopolishUp-to-dateNanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.Up-to-datehttps://github.com/jts/nanopolishnanopolishbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nanopolish
netboxr1.6.01.9.0bioconductor-netboxrTo updatenetboxr enables automated discovery of biological process modules by network analysisTo updateSystems Biologynetboxrbgruening
nextdenovo2.5.02.5.2nextdenovoTo updatenextdenovoNextDenovoDe-novo assembly, Genome assemblySequencing, Sequence assemblyString graph-based de novo assembler for long readsNextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.To updatehttps://github.com/Nextomics/NextDenovoAssemblynextdenovobgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
nucleosome_prediction3.03.0nucleosome_predictionUp-to-datePrediction of Nucleosomes Positions on the GenomeUp-to-datehttps://genie.weizmann.ac.il/software/nucleo_exe.htmlSequence Analysisnucleosome_predictionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction
numeric_clustering0.9anacondaTo updateClustering tool for numberic valuesTo updatehttp://scikit-learn.org/stable/index.htmlStatisticsnumeric_clusteringbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering
openms2.1.03.1.0openmsTo updateOpenMS in version 2.1.To updateProteomicsopenmsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/openms
pandas_rolling_window0.1numpyTo updateRolling window calculationsTo updatehttps://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.htmlStatisticspandas_rolling_windowbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window
peakachu0.2.0+galaxy10.2.0peakachuTo updatePEAKachu is a peak-caller for CLIP- and RIP-Seq dataTo updateSequence Analysis, RNApeakachurnateamhttps://github.com/tbischler/PEAKachu
perf5.11.0perfTo updatesuitable for boolean classification problemsTo updatehttp://osmot.cs.cornell.edu/kddcup/software.htmlstats_perf_toolbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/perf
pfamscan1.61.6pfam_scanUp-to-datepfamscanPfamScanProtein sequence analysisSequence analysisSearch a FASTA sequence against a library of Pfam HMM.This tool is used to search a FASTA sequence against a library of Pfam HMM.Up-to-datehttp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/Sequence Analysispfamscanbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
pg_toolspostgresqlTo updatetool suite for dealing with Postgresql databases from Galaxy's historyTo updatehttps://www.postgresql.orgData Export, Data Sourcepgtoolsbgrueninghttps://github.com/bgruening/galaxytools/tools/pgtools
pharmcatTo updatePharmacogenomics Clinical Annotation ToolTo updatehttps://pharmcat.org/Variant Analysispharmcatbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/pharmcat
piranha1.2.1.01.2.1piranhaTo updatePiranha is a peak-caller for CLIP- and RIP-Seq dataTo updateSequence Analysis, RNApiranharnateamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha
platypus0.0.11platypusTo updateefficient and accurate variant-detection in high-throughput sequencing dataTo updatehttp://www.well.ox.ac.uk/platypusSequence Analysisplatypusbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/platypus
plotly_ml_performance_plots0.2pandasTo updateperformance plots for machine learning problemsTo updatehttp://scikit-learn.org/stable/modules/classes.html#module-sklearn.metricsVisualizationplotly_ml_performance_plotsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots
plotly_parallel_coordinates_plot0.2pythonTo updateparallel coordinates plot produced with plotlyTo updatehttps://plot.ly/python/parallel-coordinates-plot/Visualizationplotly_parallel_coordinates_plotbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot
plotly_regression_performance_plots0.1pythonTo updateperformance plots for regression problemsTo updatehttp://scikit-learn.org/stable/supervised_learning.html#supervised-learningVisualizationplotly_regression_performance_plotsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots
protease_prediction0.92.0edenTo updateThis tool can learn the cleavage specificity of a given class of proteases.To updatehttps://github.com/fabriziocosta/edenSequence Analysis, Proteomicsprotease_predictionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction
protein_properties0.2.01.70biopythonTo updateCalculation of various properties from given protein sequencesTo updateSequence Analysisprotein_propertiesbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/protein_properties
improviser1.1.0.1To updateVisualisation of PepXML filesTo updatehttp://www.improviser.uni-freiburg.de/Proteomicsproteomics_improviserbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser
racon1.5.01.5.0raconUp-to-dateRaconRaconGenome assembly, Mapping assembly, Sequence trimmingWhole genome sequencing, Sequence assembly, Plant biologyConsensus module for raw de novo DNA assembly of long uncorrected reads.The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: https://github.com/isovic/racon| Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected readsUp-to-datehttps://github.com/isovic/raconSequence Analysisraconbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/racon
repeat_masker0.1.24.1.5RepeatMaskerTo updateRepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.To updatehttp://www.repeatmasker.org/Sequence Analysisrepeat_maskerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker
replaceColumn0.2To updateA tool to replace all column entries of a file given by values of a key-value file.To updateText Manipulationreplace_column_by_key_value_filebgrueninghttps://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn
rest_tool0.1.0To updateThis tool fetches data from pubchem via the PubChem REST API.To updatehttps://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.htmlData Sourcepubchem_rest_toolbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/rest_tool
antarna1.12.0.1.2antarnaTo updateantaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .To updateRNAantarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/
aresite20.1.2pythonTo updateAREsite2 REST InterfaceTo updatehttp://rna.tbi.univie.ac.at/AREsiteRNA, Data Source, Sequence Analysisaresite2rnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2
blockclust1.1.11.1.1blockclustUp-to-dateBlockClust detects transcripts with similar processing patterns.Up-to-datehttps://github.com/bgruening/galaxytools/tree/master/workflows/blockclustRNAblockclustrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust
cmsearch_deoverlap0.08+galaxy0perlTo updateremoves lower scoring overlaps from cmsearch results.To updatehttps://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.plRNAcmsearch_deoverlaprnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap
cmv1.0.81.0.8cmvUp-to-datecmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.Up-to-datehttps://github.com/eggzilla/cmvRNAcmvrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv
cofold2.0.4.02.0.4cofoldTo updateCofold predicts RNA secondary structures that takes co-transcriptional folding into account.To updatehttp://www.e-rna.org/cofold/RNAcofoldrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold
compalignp1.01.0compalignpUp-to-dateCompute fractional identity between trusted alignment and test alignmentUp-to-dateRNA, Sequence Analysiscompalignprnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/
coprarna2.1.12.1.4coprarnaTo updateTarget prediction for prokaryotic trans-acting small RNAsTo updatehttps://github.com/PatrickRWright/CopraRNARNA, Sequence Analysiscoprarnarnateamhttps://github.com/PatrickRWright/CopraRNA
dewseq0.1.0+galaxy0pythonTo updateDEWSeq is a sliding window based peak caller for eCLIP/iCLIP dataTo updatehttps://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpersSequence Analysis, RNA, CLIP-seqdewseqrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq
dorina1.0To updatedata source for RNA interactions in post-transcriptional regulationTo updateRNA, Data Sourcedorinarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/
dot2ct5.7.a6.4rnastructureTo updateDot-Bracket to Connect Table (CT)To updateSequence Analysis, RNAdot2ctrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct
dotknot1.3.1vienna_rnaTo updateDotKnot is a heuristic method for pseudoknot prediction in a given RNA sequenceTo updatehttp://dotknot.csse.uwa.edu.au/RNA, Proteomicsdotknotbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot
exparna1.0.11.0.1exparnaUp-to-dateExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.Up-to-datehttp://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jspRNAexparnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna
graphprot1.1.7+galaxy11.1.7graphprotTo updateGraphProt models binding preferences of RNA-binding proteins.To updatehttps://github.com/dmaticzka/GraphProtSequence Analysis, RNA, CLIP-seqgraphprotrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot
htseq-clip0.1.0+galaxy02.19.0b0htseq-clipTo updatehtseq-clip is a toolset for the analysis of eCLIP/iCLIP datasetsTo updatehttps://github.com/EMBL-Hentze-group/htseq-clipSequence Analysis, RNA, CLIP-seqhtseq_cliprnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip
infernal1.1.41.1.5infernalTo updateinfernalInfernalNucleic acid feature detectionSequence sites, features and motifsInfernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.To updatehttp://infernal.janelia.org/RNAinfernalbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/infernal
infornaTo updateINFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.To updatehttp://rna.informatik.uni-freiburg.de/INFORNA/Input.jspRNAinfornarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna
intarna3.4.03.4.0intarnaUp-to-dateEfficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.Up-to-datehttps://github.com/BackofenLab/IntaRNARNAintarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna
kinwalkerTo updateKinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.To updatehttp://www.bioinf.uni-leipzig.de/Software/Kinwalker/RNAkinwalkerrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker
locarna1.9.2.32.0.0locarnaTo updateLocARNA - A suite for multiple alignment and folding of RNAsTo updatehttp://www.bioinf.uni-freiburg.de/Software/LocARNA/RNAlocarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna
mea0.6.4.10.6.4meaTo updateMaximum expected accuracy predictionTo updatehttp://www.bioinf.uni-leipzig.de/Software/meaRNAmearnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea
mqc1.91.10mqcTo updateRibosome profiling mapping quality control toolTo updatehttps://github.com/Biobix/mQCSequence Analysismqcrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/
nastiseq1.01.0r-nastiseqUp-to-dateA method to identify cis-NATs using ssRNA-seqUp-to-datehttps://ohlerlab.mdc-berlin.de/software/NASTIseq_104/RNAnastiseqrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq
paralyzer1.51.5paralyzerUp-to-dateA method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.Up-to-datehttps://ohlerlab.mdc-berlin.de/software/PARalyzer_85/RNAparalyzerrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer
pipmir0.1.01.1pipmirTo updateA method to identify novel plant miRNA.To updatehttps://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/RNApipmirrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir
rRNA0.1hmmsearch3.0To updateIdentification of ribosomal RNA genes in metagenomic fragments.To updatehttp://weizhong-lab.ucsd.edu/meta_rna/RNArrnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rRNA
rbpbench0.8.10.8.1rbpbenchUp-to-daterbpbenchRBPBenchRNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysisEvaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifsEvaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifsUp-to-datehttps://github.com/michauhl/RBPBenchSequence Analysis, RNA, CLIP-seqrbpbenchrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench
rcas1.5.41.28.2bioconductor-rcasTo updateRCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experimentsTo updatehttps://github.com/BIMSBbioinfo/RCASRNArcasrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/
reago1.11.1reagoUp-to-dateReago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.Up-to-datehttps://github.com/chengyuan/reago-1.1Metagenomics, RNAreagornateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
remurna1.0.01.0remurnaTo updateremuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA ConformationTo updatehttps://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurnaRNAremurnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna
ribotaper1.3.1a1.3.1ribotaperTo updateribotaperRiboTaperGene expression profilingFunctional genomicsA method for defining traslated ORFs using Ribosome Profiling data.New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.To updatehttps://ohlerlab.mdc-berlin.de/software/RiboTaper_126/RNAribotaperrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/
rna_shapes3.3.0@EXECUTABLE@To updateCompute secondary structures of RNATo updateRNArnashapesrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes
rnabob2.2.1.02.2.1rnabobTo updateFast pattern searching for RNA structural motifsTo updatehttp://eddylab.org/software.htmlRNArnabobrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob
rnacode0.3.20.3rnacodeTo updateAnalyze the protein coding potential in MSATo updateRNArnacodernateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode
rnacommender0.1.13.5samTo updateRNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.To updatehttps://github.com/gianlucacorrado/RNAcommenderRNArnacommenderrnateamhttps://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender
rnalien1.3.61.8.0rnalienTo updateRNAlien unsupervized RNA family model constructionTo updatehttp://rna.tbi.univie.ac.at/rnalien/RNA, Sequence Analysisrnalienrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien
rnasnp1.2.01.2rnasnpTo updateRNAsnp Efficient detection of local RNA secondary structure changes induced by SNPsTo updatehttp://rth.dk/resources/rnasnp/RNArnasnprnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rnasnp
rnaz2.1.12.1.1rnazUp-to-dateRNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.Up-to-datehttps://www.tbi.univie.ac.at/~wash/RNAz/RNArnazbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz
selectsequencesfrommsa1.0.51.0.5selectsequencesfrommsaUp-to-dateSelectSequences - selects representative entries from a multiple sequence alignment in clustal formatUp-to-datehttps://github.com/eggzilla/SelectSequencesRNA, Sequence Analysisselectsequencesfrommsarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa
sortmerna4.3.64.3.6sortmernaUp-to-datesortmernaSortMeRNASequence similarity search, Sequence comparison, Sequence alignment analysisMetatranscriptomics, MetagenomicsSortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.Up-to-datehttp://bioinfo.lifl.fr/RNA/sortmerna/RNAsortmernarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna
sshmm1.0.71.0.7sshmmUp-to-datessHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq dataUp-to-datehttps://github.molgen.mpg.de/heller/ssHMMSequence Analysis, RNAsshmmrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/
targetfinder1.71.7targetfinderUp-to-datePlant small RNA target prediction toolUp-to-datehttps://github.com/carringtonlab/TargetFinder.gitRNAtargetfinderrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/
trna_prediction0.61.2.41aragornTo updateAragorn predicts tRNA and tmRNA in nucleotide sequences.To updatehttp://mbioserv2.mbioekol.lu.se/ARAGORN/RNAtrna_predictionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction
vienna_rna2.2.102.6.4viennarnaTo updateViennaRNA - Prediction and comparison of RNA secondary structuresTo updatehttp://www.tbi.univie.ac.at/RNA/RNAviennarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna
sailfish0.10.1.1bzip2To updateSailfish is a tool for transcript quantification from RNA-seq dataTo updatehttp://www.cs.cmu.edu/~ckingsf/software/sailfish/Sequence Analysis, RNAsailfishbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/sailfish
salmon1.10.11.10.2salmonTo updateSalmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.To updatehttps://github.com/COMBINE-lab/salmonSequence Analysis, RNA, Transcriptomicsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/salmon
sambamba1.0sambambaTo updateSAMBAMBA: process your BAM data faster!To updatehttps://github.com/lomereiter/sambambaSAMsambambarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/sambamba
sed0.0.1sedTo updateManipulate your data with the sed command line tool.To updatehttps://github.com/bgruening/galaxytools/tree/master/tools/sedText Manipulationsed_wrapperbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/sed
segemehl0.2.0.40.3.4segemehlTo updatesegemehl - short read mapping with gapsTo updatehttp://www.bioinf.uni-leipzig.de/Software/segemehl/Next Gen Mapperssegemehlrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/segemehl
sklearn1.0.11.0To updateMachine Learning tool suite from Scikit-learnTo updatehttp://scikit-learn.orgMachine Learning, Statisticssklearnbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/sklearn
splitfasta0.4.01.70biopythonTo updateSplit a multi-sequence fasta file into files containing single sequencesTo updateText Manipulationsplitfastarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/splitfasta
statistics0.3numpyTo updateTool for computing statistical tests.To updatehttps://github.com/bgruening/galaxytools/tree/master/tools/statisticsStatisticsbg_statistical_hypothesis_testingbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/statistics
stress_ng0.12.04stress-ngTo updatestress test a computer system in various selectable waysTo updateWeb Servicesstress_ngbgruening-utilhttps://github.com/ColinIanKing/stress-ng
tapscan4.76+galaxy03.4hmmerTo updateSearch for transcription associated proteins (TAPs)To updatehttps://plantcode.cup.uni-freiburg.de/tapscan/Proteomicstapscanbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/tapscan
add_line_to_file0.1.08.25coreutilsTo updateAdds a text line to the beginning or end of a file.To updateText Manipulationadd_line_to_filebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file
column_arrange_by_header0.2To updateColumn arrange by header nameTo updateText Manipulationcolumn_arrange_by_headerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header
join_files_on_column_fuzzy1.0.1pythonTo updateJoin two files on a common column, allowing a certain difference.To updateText Manipulationjoin_files_on_column_fuzzybgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy
split_file_on_column0.6gawkTo updateSplit a file on a specific column.To updateText Manipulationsplit_file_on_columnbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column
split_file_to_collection0.5.1pythonTo updateSplit tabular, MGF, FASTA, or FASTQ files to a dataset collection.To updateText Manipulationsplit_file_to_collectionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection
text_processing9.38.25coreutilsTo updateHigh performance text processing tools using the GNU coreutils, sed, awk and friends.To updatehttps://www.gnu.org/software/Text Manipulationtext_processingbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing
tgsgapcloser1.0.31.2.1tgsgapcloserTo updateTGS-GapCloserTGS-GapCloserGenome assembly, Read mapping, Scaffolding, Localised reassemblySequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, MappingTGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.To updatehttps://github.com/BGI-Qingdao/TGS-GapCloserAssemblytgsgapcloserbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser
tool_recommendation_model0.0.5pythonTo updateCreate model to recommend toolsTo updatehttps://github.com/bgruening/galaxytoolsMachine Learningcreate_tool_recommendation_modelbgrueninghttps://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model
trim_galore0.6.70.6.10trim-galoreTo updatetrim_galoreTrim GaloreSequence trimmingSequence analysisTrim Galore adaptive quality and adapter trimmerA wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.To updatehttp://www.bioinformatics.babraham.ac.uk/projects/trim_galore/Sequence Analysis, Fastq Manipulationtrim_galorebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
uniprot_rest_interface0.4requestsTo updateUniProt ID mapping and sequence retrievalTo updatehttps://github.com/jdrudolph/uniprotProteomics, Sequence Analysisuniprot_rest_interfacebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface
vt0.22015.11.10vtTo updateA tool set for short variant discovery in genetic sequence data.To updateSequence Analysis, Variant Analysisvtbgrueninghttps://github.com/atks/vt
wtdbg2.52.5wtdbgUp-to-datewtdbg2wtdbg2Genome assembly, De-novo assemblySequence assembly, SequencingWTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.Up-to-datehttps://github.com/ruanjue/wtdbg2Assemblywtdbgbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
align_back_trans0.0.101.70biopythonTo updateThread nucleotides onto a protein alignment (back-translation)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_transFasta Manipulation, Sequence Analysisalign_back_transpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
chromosome_diagram0.0.31.70biopythonTo updateChromosome Diagrams using BiopythonTo updateGraphics, Sequence Analysis, Visualizationchromosome_diagrampeterjc
clc_assembly_cell0.0.71.19.2samtoolsTo updateGalaxy wrapper for the CLC Assembly Cell suite from CLCBioTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cellAssembly, Next Gen Mappers, SAMclc_assembly_cellpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
clinod0.1.01.3clinodTo updateNoD: a Nucleolar localization sequence detector for eukaryotic and viral proteinsTo updatehttp://www.compbio.dundee.ac.uk/www-nod/Sequence Analysisclinodpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
count_roi_variants0.0.61.19.2samtoolsTo updateCount sequence variants in region of interest in BAM fileTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variantsAssembly, SAMcount_roi_variantspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants
coverage_stats0.1.01.19.2samtoolsTo updateBAM coverage statistics using samtools idxstats and depthTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_statsAssembly, SAMcoverage_statspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats
effectiveT30.0.201.0.1effectiveT3To updateFind bacterial type III effectors in protein sequencesTo updatehttp://effectors.orgSequence Analysiseffectivet3peterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
fasta_filter_by_id0.0.71.1.5galaxy_sequence_utilsTo updateFilter FASTA sequences by ID (DEPRECATED)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_idFasta Manipulation, Sequence Analysis, Text Manipulationfasta_filter_by_idpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id
fastq_filter_by_id0.0.71.1.5galaxy_sequence_utilsTo updateFilter FASTQ sequences by ID (DEPRECATED)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_idFastq Manipulation, Sequence Analysis, Text Manipulationfastq_filter_by_idpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id
fastq_pair_names0.0.51.1.5galaxy_sequence_utilsTo updateExtract FASTQ paired read namesTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_namesSequence Analysisfastq_pair_namespeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names
fastq_paired_unpaired0.1.51.1.5galaxy_sequence_utilsTo updateDivide FASTQ file into paired and unpaired readsTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpairedSequence Analysis, Text Manipulationfastq_paired_unpairedpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired
get_orfs_or_cdss0.2.31.70biopythonTo updateSearch nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdssSequence Analysisget_orfs_or_cdsspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss
mummer0.0.89.18ghostscriptTo updateDraw dotplots using mummer, mucmer, or promer with mummerplotTo updatehttp://mummer.sourceforge.net/Graphics, Sequence Analysis, Visualizationmummerpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/mummer
nlstradamus0.0.111.8NLStradamusTo updateFind nuclear localization signals (NLSs) in protein sequencesTo updatehttp://www.moseslab.csb.utoronto.ca/NLStradamusFasta Manipulation, Sequence Analysisnlstradamuspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus
predictnls0.0.10To updatePython reimplementation of predictNLS for GalaxyTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/predictnlsSequence Analysispredictnlspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls
protein_analysis0.0.13promoterTo updateTMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTbTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysisSequence Analysistmhmm_and_signalppeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis
sample_seqs0.2.61.70biopythonTo updateSub-sample sequences files (e.g. to reduce coverage)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqsAssembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysissample_seqspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs
samtools_depad0.0.51.19.2samtoolsTo updateRe-align a SAM/BAM file with a padded reference (using samtools depad)To updatehttp://www.htslib.org/Assembly, SAM, Sequence Analysissamtools_depadpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad
samtools_depth0.0.31.19.2samtoolsTo updateCoverage depth via samtoolsTo updatehttp://www.htslib.org/Assembly, Sequence Analysis, SAMsamtools_depthpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth
samtools_idxstats0.0.61.19.2samtoolsTo updateBAM mapping statistics (using samtools idxstats)To updatehttp://www.htslib.org/Assembly, Next Gen Mappers, SAMsamtools_idxstatspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
seq_composition0.0.51.70biopythonTo updateSequence compositionTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_compositionSequence Analysisseq_compositionpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition
seq_filter_by_id0.2.91.70biopythonTo updateFilter sequences by IDTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_idFasta Manipulation, Sequence Analysis, Text Manipulationseq_filter_by_idpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id
seq_filter_by_mapping0.0.81.70biopythonTo updateFilter sequencing reads using SAM/BAM mapping filesTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mappingAssembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysisseq_filter_by_mappingpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping
seq_length0.0.51.70biopythonTo updateCompute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_lengthFasta Manipulation, Fastq Manipulation, Sequence Analysisseq_lengthpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length
seq_primer_clip0.0.181.1.5galaxy_sequence_utilsTo updateTrim off 5' or 3' primersTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clipAssembly, Fasta Manipulation, Text Manipulationseq_primer_clippeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip
seq_rename0.0.101.1.5galaxy_sequence_utilsTo updateRename sequences with ID mapping from a tabular fileTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_renameFasta Manipulation, Sequence Analysis, Text Manipulationseq_renamepeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename
seq_select_by_id0.0.151.70biopythonTo updateSelect sequences by IDTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_idFasta Manipulation, Sequence Analysis, Text Manipulationseq_select_by_idpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id
venn_list0.1.21.1.5galaxy_sequence_utilsTo updateDraw Venn Diagram (PDF) from lists, FASTA files, etcTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/venn_listGraphics, Sequence Analysis, Visualizationvenn_listpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list
TrimNs0.1.01.0trimns_vgpTo updateTrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipelineTo updatehttps://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNsAssemblytrimnsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN
abricate1.0.11.0.1abricateUp-to-dateABRicateABRicateAntimicrobial resistance predictionGenomics, MicrobiologyMass screening of contigs for antiobiotic resistance genesMass screening of contigs for antimicrobial resistance or virulence genes.Up-to-datehttps://github.com/tseemann/abricateSequence Analysisabricateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/
abritamr1.0.141.0.14abritamrUp-to-dateA pipeline for running AMRfinderPlus and collating results into functional classesUp-to-datehttps://zenodo.org/record/7370628Sequence Analysisabritamriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr
abyss2.3.72.3.7abyssUp-to-dateabyssABySSGenome assembly, De-novo assembly, ScaffoldingSequence assemblyAssembly By Short Sequences - a de novo, parallel, paired-end sequence assemblerDe novo genome sequence assembler using short reads.Up-to-datehttp://www.bcgsc.ca/platform/bioinfo/software/abyssAssemblyabyssiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss
adapter_removal2.3.32.3.3adapterremovalUp-to-dateadapterremovalAdapterRemovalSequence trimming, Sequence merging, Primer removalRemoves residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.Up-to-datehttps://github.com/MikkelSchubert/adapterremovalFasta Manipulation, Sequence Analysisadapter_removaliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/
add_input_name_as_column0.2.0pythonTo updateAdd input name as column on an existing tabular fileTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_columnText Manipulationadd_input_name_as_columnmvdbeekhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column
aegean0.16.00.16.0aegeanUp-to-dategaevalGAEVALSequence annotationSequence analysis, Gene structureAEGeAn toolkit wrappersGene Annotation EVAluation.Up-to-datehttps://github.com/BrendelGroup/AEGeAnTranscriptomics, Sequence Analysisaegeaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean
aldex21.26.01.34.0bioconductor-aldex2To updatealdex2ALDEx2Statistical inferenceGene expression, Statistics and probabilityPerforms analysis Of differential abundance taking sample variation into accountA differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.To updatehttps://github.com/ggloor/ALDEx_biocMetagenomicsaldex2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2
allegro@VER@.03allegroTo updateallegroAllegroSequence motif discoverySequence analysis, Transcription factors and regulatory sites, DNALinkage and haplotype analysis from deCODEIt does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.To updatehttp://www.decode.com/software/Variant Analysisallegroiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/
amplican1.14.01.24.0bioconductor-amplicanTo updateamplicanamplicanAlignment, Standardisation and normalisationPCR experiment, Statistics and probabilityAmpliCan is an analysis tool for genome editing.It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.To updatehttps://github.com/valenlab/amplicanSequence Analysisamplicaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican
ampvis22.8.6To updateampvisampvisAnalysis, VisualisationBiodiversityampvis2ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.To updatehttps://github.com/MadsAlbertsen/ampvis2/Metagenomicsampvis2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2
amrfinderplus3.11.263.12.8ncbi-amrfinderplusTo updateamrfinderplusAMRFinderPlusAntimicrobial resistance predictionMicrobiology, Public health and epidemiology, Infectious disease"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms.AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organismsTo updatehttps://github.com/ncbi/amrSequence AnalysisAMRFinderPlusiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus
ancombc1.4.02.4.0bioconductor-ancombcTo updateancombcANCOMBCDNA barcodingMicrobial ecology, MetagenomicsPerforms analysis of compositions of microbiomes with bias correction.Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.To updatehttps://github.com/FrederickHuangLin/ANCOMBCMetagenomicsancombciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc
anndata0.10.30.6.22.post1anndataTo updateImport, Export, Inspect and Manipulate Anndata and Loom objectsTo updatehttps://anndata.readthedocs.ioTranscriptomics, Sequence Analysisanndataiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/
annotatemyids3.18.03.18.0bioconductor-org.hs.eg.dbUp-to-dateannotatemyidsannotatemyidsAnnotationannotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packagesThis tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.Up-to-datehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyidsGenome annotationannotatemyidsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids
arriba2.4.02.4.0arribaUp-to-dateArriba detects fusion genes in RNA-Seq data after running RNA-STARUp-to-datehttps://github.com/suhrig/arribaSequence Analysis, Transcriptomicsarribaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba
art2014.11.03.02016.06.05artTo updateartARTConversionBioinformaticsSimulator for Illumina, 454, and SOLiD sequencing dataART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiDTo updateSequence Analysis, Data Sourceartiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/art
artic1.2.4articTo updatearticARTICSequence alignmentGenomicsThe artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus buildingA bioinformatics pipeline for working with virus sequencing data sequenced with nanoporeTo updatehttps://github.com/artic-network/fieldbioinformaticsSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/artic
assembly-stats17.0217.02rjchallis-assembly-statsUp-to-dateAssembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.Up-to-datehttps://github.com/rjchallis/assembly-statsAssemblyassembly_statsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats
augustus3.4.03.5.0augustusTo updateaugustusAUGUSTUSGene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, OperationGene transcripts, Gene and protein familiesAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.To updatehttp://bioinf.uni-greifswald.de/augustus/Sequence Analysisaugustusbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus
b2btools3.0.5+galaxy03.0.6b2btoolsTo updateb2btoolsb2bToolsProtein disorder prediction, Protein secondary structure prediction, Protein feature detectionThis software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSATo updatehttps://bio2byte.beComputational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biologyiuc
bakta1.9.21.9.2baktaUp-to-dateBaktaBaktaGenome annotationGenomics, Data submission, annotation and curation, Sequence analysis"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."Rapid & standardized annotation of bacterial genomes, MAGs & plasmidsUp-to-datehttps://github.com/oschwengers/baktaSequence Analysisbaktaiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta
bam_to_scidx1.0.1openjdkTo updateContains a tool that converts a BAM file to an ScIdx file.To updatehttps://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidxConvert Formatsbam_to_scidxiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx
bamutil1.0.15bamutilTo updatebamUtil is a repository that contains several programs that perform operations on SAM/BAM files.To updatehttps://github.com/statgen/bamUtilSequence Analysisbamutiliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil
bandage2022.092022.09bandage_ngUp-to-datebandageBandageSequence assembly visualisationGenomics, Sequence assemblyBandage - A Bioinformatics Application for Navigating De novo Assembly Graphs EasilyGUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.Up-to-datehttps://github.com/rrwick/BandageVisualizationbandageiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage
barcode_splitter0.18.4.00.18.6barcode_splitterTo updateA utility to split sequence files using multiple sets of barcodesTo updatehttps://bitbucket.org/princeton_genomics/barcode_splitter/Fastq Manipulationbarcode_splitteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter
baredsc1.1.21.1.2baredscUp-to-datebaredscbaredSCData retrieval, Expression correlation analysis, Differential gene expression profilingRNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probabilitybaredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.Up-to-datehttps://github.com/lldelisle/baredSCTranscriptomics, Visualizationbaredsciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc
barrnap1.2.20.9barrnapTo updatebarrnapBarrnapGene predictionGenomics, Model organisms, Model organismsContains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).To updateSequence Analysisbarrnapiuc
basil1.2.01.2.0anise_basilUp-to-dateBreakpoint detection, including large insertionsUp-to-datehttps://github.com/seqan/anise_basilVariant Analysisbasiliuc
bax2bam0.0.110.0.11bax2bamUp-to-dateBAX to BAM converterUp-to-datehttps://github.com/pacificbiosciences/bax2bam/Convert Formats, Sequence Analysisbax2bamiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam
bayescan2.12.0.1bayescanTo updatebayescanBayeScanStatistical inferenceGenetics, Evolutionary biology, Statistics and probability, DNA polymorphismDetecting natural selection from population-based genetic dataBAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.To updatehttp://cmpg.unibe.ch/software/BayeScan/index.htmlSequence Analysisbayescaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/
bbtools39.0639.06bbmapUp-to-dateBBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.Up-to-datehttps://jgi.doe.gov/data-and-tools/bbtools/Sequence Analysisbbtoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools
bcftools1.15.11.19bcftoolsTo updatebcftoolsBCFtoolsData handling, Variant callingGenetic variation, DNA polymorphism, GWAS study, Genotyping experimentBCFtools toolkit wrappersBCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.To updatehttps://samtools.github.io/bcftools/Variant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools
bctools0.2.20.2.2bctoolsUp-to-datebctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0Up-to-datehttps://github.com/dmaticzka/bctoolsSequence Analysis, Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
beacon22.0.02.0.0beacon2-ri-toolsUp-to-dateGA4GH Beaconbeacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).Up-to-datehttps://github.com/EGA-archive/beacon2-ri-tools/tree/mainVariant Analysisbeacon2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2
beagle5.2_21Apr21.3045.4_22Jul22.46ebeagleTo updateBeagle is a program for phasing and imputing missing genotypes.To updatehttps://faculty.washington.edu/browning/beagle/beagle.htmlVariant Analysisbeagleiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle
bedops2.4.412.4.41bedopsUp-to-dateBEDOPS: high-performance genomic feature operationsUp-to-datehttps://bedops.readthedocs.io/en/latest/Genomic Interval Operationsbedops_sortbediuchttps://bedops.readthedocs.io/
bedtools2.30.02.31.1bedtoolsTo updatebedtoolsBEDToolsMappingGenomicsbedtools is a powerful toolset for genome arithmeticBEDTools is an extensive suite of utilities for comparing genomic features in BED format.To updatehttps://github.com/arq5x/bedtools2Genomic Interval Operations, Text Manipulationbedtoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
bellerophon1.01.0bellerophonUp-to-dateFilter mapped reads where the mapping spans a junction, retaining the 5-prime read.Up-to-datehttps://github.com/davebx/bellerophonSequence Analysisbellerophoniuchttps://github.com/davebx/bellerophon
berokka0.2.30.2.3berokkaUp-to-dateBerokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.Up-to-datehttps://github.com/tseemann/berokkaFasta Manipulationberokkaiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka
bigscape1.1.91.1.9bigscapeUp-to-dateConstruct sequence similarity networks of BGCs and groups them into GCFUp-to-datehttps://github.com/medema-group/BiG-SCAPEMetagenomicsbigscapeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/
binning_refiner1.4.31.4.3binning_refinerUp-to-datebinning_refinerBinning_refinerRead binning, Sequence clusteringMetagenomicsReconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.Improving genome bins through the combination of different binning programsUp-to-datehttps://github.com/songweizhi/Binning_refinerMetagenomicsbinning_refineriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/
bioext0.21.20.21.2python-bioextUp-to-dateA suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!Up-to-datehttps://pypi.python.org/pypi/biopython-extensions/Next Gen Mappersiuchttps://github.com/davebx/bioext-gx/
bioinformatics_cafe0.1.0pythonTo updateMiscellanea of scripts for bioinformaticsTo updatehttps://github.com/dariober/bioinformatics-cafe/Sequence Analysisbioinformatics_cafembernthttps://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe
biom_format2.1.152.1.7biom-formatTo updatebiomformatbiomformatFormattingLaboratory information management, Sequence analysisThe biom-format package provides a command line interface and Python API for working with BIOM files.This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.To updatehttps://github.com/biocore/biom-formatMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format
bioperl1.11.7.8perl-bioperlTo updatebioperlBioPerlData handling, Service invocationGenomics, Software engineering, Data managementConverts GenBank format files to GFF3A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.To updatehttps://bioperl.org/Sequence Analysisbp_genbank2gff3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl
biscot2.3.32.3.3biscotUp-to-dateBionano scaffolding correction toolUp-to-datehttps://github.com/institut-de-genomique/biscotAssemblybiscotiuchttps://github.com/bgruening/iuc/tree/master/tools/biscot
blast1.7.01.7.0magicblastUp-to-dateMaps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptomeUp-to-datehttps://ncbi.github.io/magicblast/Next Gen Mappersmagicblastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/blast
blastxml_to_gapped_gff31.10.6.6bcbiogffTo updateBlastXML to gapped GFF3To updateConvert Formats, Sequence Analysisblastxml_to_gapped_gff3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3
bowtie22.5.32.5.3bowtie2Up-to-datebowtie2Bowtie 2Read mappingMapping, Genomics, MappingBowtie2: Fast and sensitive read alignmentBowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.Up-to-datehttp://bowtie-bio.sourceforge.net/bowtie2Next Gen Mappersbowtie2devteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2
bracken2.92.9brackenUp-to-datebrackenBrackenStatistical calculationMetagenomics, Microbial ecologyBayesian Reestimation of Abundance with KrakENStatistical method that computes the abundance of species in DNA sequences from a metagenomics sample.Up-to-datehttps://ccb.jhu.edu/software/bracken/Sequence Analysis, Metagenomicsbrackeniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken
breseq0.35.50.38.3breseqTo updatebreseqbreseqPolymorphism detectionSequencing, Sequence analysis, DNA mutationPredicts mutations in microbial genomesRuns Breseq software on a set of fastq files.To updatehttps://github.com/barricklab/breseqVariant Analysisbreseqiuc
busco5.5.05.6.1buscoTo updatebuscoBUSCOSequence assembly validation, Scaffolding, Genome assembly, Transcriptome assemblySequence assembly, Genomics, Transcriptomics, Sequence analysisBUSCO assess genome and annotation completenessProvides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.To updatehttps://gitlab.com/ezlab/busco/-/releasesSequence Analysisbuscoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/
bwa0.7.170.7.17bwaUp-to-datebwaBWAGenome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignmentMappingWrapper for bwa mem, aln, sampe, and samseFast, accurate, memory-efficient aligner for short and long sequencing readsUp-to-datehttp://bio-bwa.sourceforge.net/Next Gen Mappersbwadevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa
bwa_mem22.2.12.2.1bwa-mem2Up-to-datebwa-mem2Bwa-mem2Sequence alignmentMappingBwa-mem2 is the next version of the bwa-mem algorithm in bwa.Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.Up-to-datehttps://github.com/bwa-mem2/bwa-mem2Next Gen Mappersbwa_mem2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2
bwameth0.2.60.2.7bwamethTo updateFast and accurate alignment of BS-seq readsTo updatehttps://github.com/brentp/bwa-methSequence Analysis, Next Gen Mappersbwamethiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth
cactus2.7.1To updatecactusCactusMultiple sequence alignment, Genome alignmentGenomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, PhylogeneticsCactus is a reference-free whole-genome multiple alignment programCactus is a reference-free whole-genome multiple alignment program.To updatehttps://github.com/ComparativeGenomicsToolkit/cactusSequence Analysiscactusgalaxy-australiahttps://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus
calculate_contrast_threshold1.0.0numpyTo updateCalculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.To updatehttps://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_thresholdVisualization, Genomic Interval Operations, SAMcalculate_contrast_thresholdiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold
calculate_numeric_param0.1.0To updateCalculate a numeric parameter value using integer and float values.To updateText Manipulationcalculate_numeric_paramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param
cat5.2.35.3catTo updatecat_binsCAT and BATTaxonomic classification, Sequence assembly, Coding region predictionMetagenomics, Metagenomic sequencing, Taxonomy, Sequence assemblyContig Annotation Tool (CAT)Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.To updatehttps://github.com/dutilh/CATMetagenomicscontig_annotation_tooliuchttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat
cdhit4.8.14.8.1cd-hitUp-to-datecd-hitcd-hitSequence clusteringSequencingCluster or compare biological sequence datasetsCluster a nucleotide dataset into representative sequences.Up-to-datehttp://weizhongli-lab.org/cd-hit/Sequence Analysis, Fasta Manipulationcd_hitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit
cemitool1.18.11.26.0bioconductor-cemitoolTo updatecemitoolCEMiToolEnrichment analysis, Pathway or network analysisGene expression, Transcriptomics, Microarray experimentGene co-expression network analysis toolIt unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.To updatehttps://www.bioconductor.org/packages/release/bioc/html/CEMiTool.htmlTranscriptomics, RNA, Statisticscemitooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool
charts1.0.1r-getoptTo updateEnables advanced visualization options in Galaxy ChartsTo updateVisualizationchartsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/
checkm1.2.01.2.2checkm-genomeTo updatecheckmCheckMOperationGenomics, Phylogenomics, Phylogenetics, Taxonomy, MetagenomicsAssess the quality of microbial genomes recovered from isolates, single cells, and metagenomesCheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.To updatehttps://github.com/Ecogenomics/CheckMMetagenomicscheckmiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm
cherri0.70.8cherriTo updatecherricherriMolecular interactions, pathways and networks, Structure analysis, Machine learningComputational Help Evaluating RNA-RNA interactionsCheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.To updatehttps://github.com/BackofenLab/CherriTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri
chira1.4.31.4.3chiraUp-to-datechiraChiRARNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNAChimeric Read Annotator for RNA-RNA interactome dataChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.Up-to-datehttps://github.com/pavanvidem/chiraRNA, Transcriptomics, Sequence Analysischiraiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/chira
chopin21.0.7chopin2To updateDomain-Agnostic Supervised Learning with Hyperdimensional ComputingTo updatehttps://github.com/cumbof/chopin2Machine Learningchopin2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2
chromeister1.5.a1.5.achromeisterUp-to-dateultra-fast pairwise genome comparisonsUp-to-datehttps://github.com/estebanpw/chromeisterSequence Analysischromeisteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister
circexplorer22.3.82.3.8circexplorer2Up-to-datecircexplorer2CIRCexplorer2RNA splicing, Gene transcripts, Literature and languageComprehensive and integrative circular RNA analysis toolset.Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.Up-to-datehttps://github.com/YangLab/CIRCexplorer2RNA, Assemblycircexplorer2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2
circos0.69.80.69.9circosTo updategalactic_circosGalactic CircosSequence visualisationBuild Circos Plots in GalaxyGalactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.To updatehttp://circos.ca/Graphicscircosiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/circos
cite_seq_count1.4.41.4.4cite-seq-countUp-to-dateCITE-seq-CountCITE-seq-CountRNA-Seq quantificationTranscriptomics, Immunoproteins and antigensCount CMO/HTOTool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.Up-to-datehttps://github.com/Hoohm/CITE-seq-CountTranscriptomicscite_seq_countiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count
clair30.1.121.0.5clair3To updateclair3Clair3Variant callingMolecular geneticsSymphonizing pileup and full-alignment for high-performance long-read variant callingClair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.To updatehttps://github.com/HKU-BAL/Clair3Sequence Analysis, Variant Analysisclair3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3
clustalw2.12.1clustalwUp-to-date\n clustal2\nClustalW multiple sequence alignment program for DNA or proteinsUp-to-datehttp://www.clustal.org/clustal2/Phylogenetics, Sequence Analysisclustalwdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw
cnv-phenopacket1.0.2cnv-phenopacketTo updatecnv-phenopacket Converts TSV metadata file to JSON.To updatehttps://pypi.org/project/cnv-phenopacket/Variant Analysiscnv_phenopacketiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket
cnv-vcf2json1.0.4cnv-vcf2jsonTo updatecnv-vcf2json Converts structural variants VCF file to JSON.To updatehttps://pypi.org/project/cnv-phenopacket/Variant Analysiscnv-vcf2jsoniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json
cnvkit0.9.100.9.10cnvkitUp-to-datecnvkitCNVkitVariant callingDNA structural variationdetecting copy number variants and alterations genome-wide from high-throughput sequencingCNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.Up-to-datehttps://github.com/etal/cnvkitVariant Analysiscnvkitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit
codeml4.94.10.7pamlTo updatepamlPAMLProbabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysisPhylogenetics, Sequence analysisDetects positive selectionPackage of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.To updatehttp://abacus.gene.ucl.ac.uk/software/paml.htmlPhylogeneticscodemliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml
cojac0.9.10.9.1cojacUp-to-datecojacCOJACGenetic variationco-occurrence of mutations on ampliconsCoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.Up-to-datehttps://github.com/cbg-ethz/cojacMetagenomics, Sequence Analysiscojaciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac
colibread24.7.14+galaxy024.7.14commetTo updateColib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genomeTo updatehttps://colibread.inria.fr/Sequence Analysis, Variant Analysiscolibreadiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread
collection_column_join0.0.38.25coreutilsTo updateColumn Join on CollectionsTo updateText Manipulationcollection_column_joiniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join
collection_element_identifiers0.0.2To updateExtract element identifiers of a collectionTo updateText Manipulationcollection_element_identifiersiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers
column_maker2.0pythonTo updateCompute an expression on every rowTo updateText Manipulationcolumn_makerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker
column_order_header_sort0.0.1pythonTo updateSort Column Order by headingTo updateText Manipulationcolumn_order_header_sortiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort
column_remove_by_header1.0pythonTo updateRemove columns by headerTo updateText Manipulationcolumn_remove_by_headeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header
compleasm0.2.50.2.5compleasmUp-to-dateCompleasm: a faster and more accurate reimplementation of BUSCOUp-to-datehttps://github.com/huangnengCSU/compleasmSequence Analysiscompleasmiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/
compose_text_param0.1.1To updateCompose a text parameter value using text, integer and float valuesTo updateText Manipulationcompose_text_paramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param
compress_file0.1.0gzipTo updateCompress files.To updateText Manipulationcompress_fileiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file
concoct1.1.01.1.0concoctUp-to-dateconcoctCONCOCTSequence clustering, Read binningMetagenomicsCONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.Up-to-datehttps://github.com/BinPro/CONCOCTMetagenomicsconcoctiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct
coverage_report0.0.41.76perl-number-formatTo updateGenerate Detailed Coverage Report from BAM fileTo updatehttps://github.com/galaxyproject/tools-iucSequence Analysiscoverage_reportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report
coverm0.7.00.7.0covermUp-to-datecovermCoverMLocal alignmentBioinformaticsCoverM genome and contig wrappersRead coverage calculator for metagenomicsUp-to-datehttps://github.com/wwood/CoverMSequence Analysiscovermiuchttps://github.com/galaxyproject/tools-iuc/tools/coverm
crispr_studio1+galaxy01crispr_studioTo updateCRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.To updatehttps://github.com/moineaulab/CRISPRStudioSequence Analysiscrispr_studioiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/
crosscontamination_barcode_filter0.32.2.1r-ggplot2To updateBarcode contamination discovery toolTo updateTranscriptomics, Visualizationcrosscontamination_barcode_filteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter
crossmap0.6.10.7.0crossmapTo updateCrossMap converts genome coordinates or annotation files between genome assembliesTo updatehttp://crossmap.sourceforge.net/Convert Formats, Genomic Interval Operationscrossmapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap
cutadapt4.64.6cutadaptUp-to-datecutadaptCutadaptSequence trimmingGenomics, Probes and primers, SequencingFlexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.Up-to-datehttps://cutadapt.readthedocs.org/en/stable/Fasta Manipulation, Fastq Manipulation, Sequence Analysiscutadaptlparsonshttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt
cutesv1.0.82.1.0cutesvTo updatecuteSVcuteSVSplit read mapping, Genotyping, Structural variation detectionDNA structural variation, Sequencing, Computer scienceLong-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysisTo updatehttps://github.com/tjiangHIT/cuteSVVariant Analysiscutesviuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv
cwpair21.1.1matplotlibTo updateContains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.To updateChIP-seqcwpair2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2
dada21.30.0bioconductor-dada2To updatedada2dada2Variant calling, DNA barcodingSequencing, Genetic variation, Microbial ecology, MetagenomicsDADA2 wrappersThis package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.To updatehttps://benjjneb.github.io/dada2/index.htmlMetagenomicsdada2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2
das_tool1.1.71.1.7das_toolUp-to-datedastooldastoolRead binningMetagenomicsDAS Tool for genome resolved metagenomicsDAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.Up-to-datehttps://github.com/cmks/DAS_ToolMetagenomicsdas_tooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool
data_source_iris_tcga1.0.0pythonTo updateIRIS-TCGA Data source toolTo updateData Sourcedata_source_iris_tcgaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga
datamash1.81.1.0datamashTo updateGNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.To updatehttps://www.gnu.org/software/datamash/Text Manipulationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash
decontaminator1.0.0numpyTo updatedecontaminatorDeep Learning method for novel virus detection in sequencing dataTo updatehttps://github.com/cbib/decontaminatorMachine Learningdecontaminatoriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator
deepmicro1.41.4deepmicroUp-to-date\n DeepMicro\nRepresentation learning and classification frameworkUp-to-datehttps://github.com/paulzierep/DeepMicroMachine Learningdeepmicroiuchttps://github.com/paulzierep/DeepMicro
deepsig1.2.51.2.5deepsigUp-to-datePredictor of signal peptides in proteins based on deep learningUp-to-datehttps://github.com/BolognaBiocomp/deepsigGenome annotationdeepsigiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig
deepvariant1.5.0To updateDeepVariant is a deep learning-based variant callerTo updatehttps://github.com/google/deepvariantVariant Analysisdeepvariantiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant
deg_annotate1.1.02.31.1bedtoolsTo updateAnnotate DESeq2/DEXSeq output tablesTo updateTranscriptomicsdeg_annotateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate
delly0.9.11.2.6dellyTo updatedelly2Delly2Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysisDNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseasesDelly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.To updatehttps://github.com/dellytools/dellyVariant Analysisdellyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/delly
deseq22.11.40.81.42.0bioconductor-deseq2To updateDESeq2DESeq2Differential gene expression analysisTranscriptomicsDifferential gene expression analysis based on the negative binomial distributionR/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.To updatehttps://www.bioconductor.org/packages/release/bioc/html/DESeq2.htmlTranscriptomics, RNA, Statisticsdeseq2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2
dexseq1.441.48.0bioconductor-dexseqTo updatedexseqDEXSeqEnrichment analysis, Exonic splicing enhancer predictionRNA-SeqInference of differential exon usage in RNA-SeqThe package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.To updatehttps://www.bioconductor.org/packages/release/bioc/html/DEXSeq.htmlTranscriptomics, RNA, Statisticsdexseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq
diamond2.0.152.1.9diamondTo updatediamondDiamondSequence alignment analysisSequence analysis, ProteinsDIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.To updatehttps://github.com/bbuchfink/diamondSequence Analysisdiamondbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond
diffbind2.10.03.12.0bioconductor-diffbindTo updatediffbindDiffBindDifferential binding analysisChIP-seqDiffbind provides functions for processing ChIP-Seq data.Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.To updatehttp://bioconductor.org/packages/release/bioc/html/DiffBind.htmlChIP-seqdiffbindbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind
dimet0.2.10.2.2dimetTo updateDIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.To updatehttps://github.com/cbib/DIMetMetabolomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet
disco1.2discoTo updatediscoDISCOProtein sequence analysisStructure determinationDISCO is a overlap-layout-consensus (OLC) metagenome assemblerDISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.To updatehttp://disco.omicsbio.org/Metagenomics, Assemblydiscoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/
dnabot3.1.0dnabotTo updateDNA assembly using BASIC on OpenTronsTo updatehttps://github.com/BASIC-DNA-ASSEMBLY/DNA-BOTSynthetic Biologydnabotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot
dnaweaver1.0.21.0.2dnaweaver_synbiocadUp-to-dateGiven a SBOL input, calculate assembly parts for Gibson or Golden Gate.Up-to-datehttps://github.com/Edinburgh-Genome-Foundry/DnaWeaverSynthetic Biologydnaweaveriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver
dram1.3.51.4.6dramTo updatedramDRAMGene functional annotationMetagenomics, Biological databases, Molecular geneticsDRAM for distilling microbial metabolism to automate the curation of microbiome functionDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomesTo updatehttps://github.com/WrightonLabCSU/DRAMMetagenomicsdramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dram
drep3.4.53.5.0drepTo updatedrepdRepGenome comparisonMetagenomics, Genomics, Sequence analysisdRep compares and dereplicates genome setsFast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.To updatehttps://github.com/MrOlm/drepMetagenomicsdrepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/drep
dropletutils1.10.01.22.0bioconductor-dropletutilsTo updatedropletutilsDropletUtilsLoading, Community profilingGene expression, RNA-seq, Sequencing, TranscriptomicsDropletUtils - Utilities for handling droplet-based single-cell RNA-seq dataProvides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.To updatehttps://bioconductor.org/packages/devel/bioc/html/DropletUtils.htmlTranscriptomics, Sequence Analysisdropletutilsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/
ebi_tools0.1.0sixTo updateTools to query and download data from several EMBL-EBI databasesTo updatehttp://www.ebi.ac.uk/services/allWeb Services, Data Sourceebi_toolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools
edger3.36.04.0.2bioconductor-edgerTo updateedgeredgeRDifferential gene expression analysisGenetics, RNA-Seq, ChIP-seqPerform RNA-Seq differential expression analysis using edgeR pipelineDifferential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.To updatehttp://bioconductor.org/packages/release/bioc/html/edgeR.htmlTranscriptomics, RNA, Statisticsedgeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/edger
egsea1.20.01.28.0bioconductor-egseaTo updateegseaEGSEAGene set testingSystems biologyThis tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testingThis package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.To updatehttps://bioconductor.org/packages/release/bioc/html/EGSEA.htmlTranscriptomics, RNA, Statisticsegseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea
emboss_55.0.06.6.0embossTo updateembossEMBOSSSequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignmentMolecular biology, Sequence analysis, BiologyGalaxy wrappers for EMBOSS version 5.0.0 toolsDiverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.To updatehttp://emboss.open-bio.org/Sequence Analysis, Fasta Manipulationemboss_5devteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5
ena_upload0.6.30.7.1ena-upload-cliTo updateSubmits experimental data and respective metadata to the European Nucleotide Archive (ENA).To updatehttps://github.com/usegalaxy-eu/ena-upload-cliData Exportena_uploadiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload
enasearch0.2.2enasearchTo updateA Python library for interacting with ENA's APITo updatehttps://github.com/bebatut/enasearchData Sourceenasearchiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch
ensembl_vep110.1111.0ensembl-vepTo updateEnsembl VEP: Annotate VCFs with variant effect predictionsTo updatehttps://github.com/Ensembl/ensembl-vepVariant Analysisensembl_vepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep
episcanpy0.3.20.4.0episcanpyTo updateepiscanpyepiScanpyEnrichment analysis, ImputationEpigenomics, Cell biology, DNAEpiScanpy – Epigenomics single cell analysis in pythonEpigenomics Single Cell Analysis in Python.To updatehttps://github.com/colomemaria/epiScanpyEpigeneticsepiscanpyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/
exomedepth1.1.01.1.16r-exomedepthTo updateexomedepthExomeDepthSequence analysis, Variant calling, Genotyping, Copy number estimationExome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseasesExomeDepth: Calls copy number variants (CNVs) from targeted sequence dataCopy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.To updatehttps://cran.r-project.org/package=ExomeDepthSequence Analysis, Variant Analysisexomedepthcrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth
exonerate2.4.02.4.0exonerateUp-to-dateexonerateExoneratePairwise sequence alignment, Protein threading, Genome alignmentSequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networksExonerate is a generic tool for pairwise sequence comparison.A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.Up-to-datehttps://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerateSequence Analysisexonerateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate
export2graphlan0.200.22export2graphlanTo updateexport2graphlanexport2graphlanConversionTaxonomy, Metabolomics, Biomarkersexport2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAnexport2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.To updatehttps://bitbucket.org/CibioCM/export2graphlan/overviewMetagenomicsexport2graphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/
extract_genomic_dna3.0.3+galaxy20.11.0bx-pythonTo updateContains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.To updateGenomic Interval Operationsextract_genomic_dnaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna
fargene0.10.1fargeneUp-to-datefargenefARGeneAntimicrobial resistance predictionMetagenomics, Microbiology, Public health and epidemiologyfARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.Up-to-datehttps://github.com/fannyhb/fargeneSequence Analysisfargeneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene
fasta_nucleotide_color_plot1.0.1openjdkTo updateContains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.To updatehttps://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplotVisualizationfasta_nucleotide_color_plotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot
fasta_stats2.0numpyTo updateDisplay summary statistics for a fasta file.To updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/Sequence Analysisfasta_statsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/
fastani1.31.34fastaniTo updateFast alignment-free computation of whole-genome Average Nucleotide IdentityTo updatehttps://github.com/ParBLiSS/FastANISequence Analysisfastaniiuc
fastp0.23.4fastpTo update\n fastp\nFast all-in-one preprocessing for FASTQ filesTo updatehttps://github.com/OpenGene/fastpSequence Analysisfastpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp
fastqc0.74+galaxy00.12.1fastqcTo updatefastqcFastQCSequence composition calculation, Sequencing quality control, Statistical calculationSequencing, Data quality management, Sequence analysisRead QC reports using FastQCThis tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.To updatehttp://www.bioinformatics.babraham.ac.uk/projects/fastqc/Fastq Manipulationfastqcdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc
fastqe0.3.1+galaxy00.3.1fastqeTo updatefastqeFASTQESequencing quality controlSequence analysis, SequencingFASTQECompute quality stats for FASTQ files and print those stats as emoji... for some reason.To updatehttps://fastqe.com/Sequence Analysisfastqeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe
fasttree2.1.102.1.11fasttreeTo updatefasttreeFastTreePhylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)Phylogenetics, Sequence analysisFastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVLInfers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.To updatehttp://www.microbesonline.org/fasttree/Phylogeneticsfasttreeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree
featurecounts2.0.32.0.6subreadTo updatefeaturecountsFeatureCountsRead summarisationSequencingfeatureCounts counts the number of reads aligned to defined masked regions in a reference genomefeatureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.To updatehttp://bioinf.wehi.edu.au/featureCountsRNA, Transcriptomics, Sequence Analysisfeaturecountsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts
feelnc0.2.10.2feelncTo updatefeelncFEELncAnnotation, ClassificationRNA-seq, Functional, regulatory and non-coding RNAGalaxy wrapper for FEELncA tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.To updatehttps://github.com/tderrien/FEELncSequence Analysisfeelnciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc
fermikitr193r193fermi2Up-to-dateFermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.Up-to-datehttps://github.com/lh3/fermikitAssembly, Variant Analysisfermikitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit
fgsea1.8.0+galaxy11.28.0bioconductor-fgseaTo updatefgseafgseaGene-set enrichment analysisGeneticsPerform gene set testing using fgseaThe package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.To updatehttps://bioconductor.org/packages/release/bioc/html/fgsea.htmlVisualization, Transcriptomics, Statisticsfgseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea
filtlong0.2.10.2.1filtlongUp-to-date\n filtlong\nFiltlong - Filtering long reads by qualityUp-to-datehttps://github.com/rrwick/FiltlongFastq Manipulation, Sequence Analysisfiltlongiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong
flair1.52.0.0flairTo updateFLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.To updatehttps://github.com/BrooksLabUCSC/flairNanoporeflairiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/flair
flash1.2.111.2.11flashUp-to-dateflashFLASHRead pre-processing, Sequence merging, Sequence assemblySequencing, Sequence assemblyFast Length Adjustment of SHort readsIdentifies paired-end reads which overlap in the middle, converting them to single long readsUp-to-datehttps://ccb.jhu.edu/software/FLASH/Assembly, Fastq Manipulationflashiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/flash
fraggenescan1.31fraggenescanTo updatefraggenescanFragGeneScanGene predictionGenetics, Sequence analysisTool for finding (fragmented) genes in short readApplication for finding (fragmented) genes in short readsTo updatehttps://sourceforge.net/projects/fraggenescan/Sequence Analysisfraggenescaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/
freebayes1.3.61.3.7freebayesTo updatefreebayesFreeBayesVariant calling, Statistical calculationGenomics, Genetic variation, Rare diseasesGalaxy Freebayes Bayesian genetic variant detector toolBayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.To updatehttps://github.com/ekg/freebayesVariant Analysisfreebayesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes
freec11.6gawkTo updatefreecFREECCopy number estimation, Variant calling, Genome alignmentDNA structural variation, Oncology, Human genetics, Data miningControl-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.To updatehttp://boevalab.inf.ethz.ch/FREEC/Variant Analysiscontrol_freeciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/freec
freyja1.4.41.4.9freyjaTo updatefreyjalineage abundances estimationTo updatehttps://github.com/andersen-lab/FreyjaMetagenomics, Sequence Analysisfreyjaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja
fsd1.0.2matplotlibTo updateTool that plots a histogram of sizes of read familiesTo updateGraphicsduplex_family_size_distributioniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd
funannotate1.8.15To update\n funannotate\nFunannotate is a genome prediction, annotation, and comparison software package.To updatehttps://funannotate.readthedocs.ioGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate
gatk44.1.7.04.5.0.0gatk4To updateA Galaxy wrapper for Mutect2 from GATKTo updatehttps://software.broadinstitute.org/gatk/gatk4Variant Analysisgatk4_mutect2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4
gdcwebapp1.0.0pythonTo updateGDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED formatTo updatehttp://bioinf.iasi.cnr.it/gdcwebapp/Data Source, Convert Formatsgdcwebappiuchttps://github.com/fabio-cumbo/GDCWebApp4Galaxy
gecko1.21.2geckoUp-to-dateUngapped genome comparisonUp-to-datehttps://github.com/otorreno/geckoSequence Analysisgeckoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko
gemini0.20.10.30.2geminiTo updategeminiGEMINISequence analysis, Genetic variation analysisSequence analysisGEMINI: a flexible framework for exploring genome variationGEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.To updatehttps://github.com/arq5x/geminiSequence Analysis, Next Gen Mappersgeminiiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini
genebed_maf_to_fasta1.0.1+galaxy0To updateStitch gene blocks given a set of coding exon intervalsTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/Genomic Interval Operationsgenebed_maf_to_fastaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/
genehunter_modscore3.0.03.1ghmTo updateMaximised LOD score pedigree analysis utilityTo updatehttps://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.htmlVariant Analysisgenehunter_modscoreiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/
geneiobio4.7.1+galaxy1To updateGene.iobio is an interactive tool for variant and trio analysis.To updatehttps://github.com/iobio/gene.iobioSequence Analysisgeneiobioiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio
genetracknumpyTo updateContains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand.To updateChIP-seqgenetrackiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack
genomescope2.02.0genomescope2Up-to-dateAnalyze unassembled short readsUp-to-datehttps://github.com/tbenavi1/genomescope2.0Statisticsgenomescopeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope
genomic_super_signature1.2.01.10.0bioconductor-genomicsupersignatureTo updategenomicsupersignatureGenomicSuperSignatureGene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reductionRNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experimentInterpretation of RNAseq experiments through robust, efficient comparison to public databasesGenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.To updatehttps://github.com/shbrief/GenomicSuperSignatureSequence Analysis, RNA, Transcriptomicsgenomic_super_signatureiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature
genrich0.5+galaxy20.6.1genrichTo updateGenrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).To updatehttps://github.com/jsh58/GenrichChIP-seqgenrichiuchttps://github.com/jsh58/Genrich
get_hrun0.5.9.20.8.1.1pyfaidxTo updateAnnotate indel variants with homopolymer contextTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrunVariant Analysisget_hruniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun
getorganelle1.7.7.01.7.7.0getorganelleUp-to-dategetorganelleGetOrganelleDe-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimmingCell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organismsGetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.Up-to-datehttps://github.com/Kinggerm/GetOrganelleAssemblygetorganelleiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle
gfa_to_fa0.1.2To updategfa_to_fa - Converting GFA format to Fasta formatTo updatehttp://gfa-spec.github.io/GFA-spec/Convert Formatsgfa_to_faiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa
gff3_rebase1.20.6.6bcbiogffTo updateRebase a GFF against a parent GFF (e.g. an original genome)To updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebaseSequence Analysisgff3_rebaseiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase
gffcompare0.12.60.12.6gffcompareUp-to-dategffcomparegffcompareSequence annotationNucleic acids, Sequence analysisGalaxy wrappers for Geo Pertea's GffCompare package.Program for comparing, annotating, merging and tracking transcripts in GFF files.Up-to-datehttps://github.com/gpertea/gffcompare/Transcriptomicsgffcompareiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare
gffread0.12.70.12.7gffreadUp-to-dategffreadgffreadSequence annotationNucleic acids, Sequence analysisgffread filters and/or converts GFF3/GTF2 recordsprogram for filtering, converting and manipulating GFF filesUp-to-datehttp://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/Sequence Analysisgffreaddevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread
ggplot23.4.0r-baseTo updateggplot2ggplot2VisualisationData visualisationggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.Plotting system for R, based on the grammar of graphics.To updatehttps://github.com/tidyverse/ggplot2Visualizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2
ggupset1.0r-ggupsetTo updateCreate Upset Plots with ggupsetTo updatehttps://github.com/const-ae/ggupsetGraphicsggupsetiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset
glimmer3.02glimmerTo updategeminiGEMINISequence analysis, Genetic variation analysisSequence analysisGlimmer makes gene predictions.GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.To updatehttps://ccb.jhu.edu/software/glimmer/Sequence Analysisbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer
goenrichment2.0.12.0.1goenrichmentUp-to-dategoenrichmentGOEnrichmentGene-set enrichment analysisTranscriptomicsPerforms GO Enrichment analysis.GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.Up-to-datehttps://github.com/DanFaria/GOEnrichmentGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment
goseq1.50.01.54.0bioconductor-goseqTo updategoseqGOseqGene functional annotationRNA-Seqgoseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq dataDetect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.To updatehttps://bioconductor.org/packages/release/bioc/html/goseq.htmlStatistics, RNA, Micro-array Analysisgoseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq
gprofiler@TOOL_VERSION@+galaxy11r-gprofiler2To updatefunctional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and moreTo updatehttps://biit.cs.ut.ee/gprofilerStatistics, Web Servicesgprofileriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/
graphembed2.42.4graph_embedUp-to-dateCompute a 2D embedding of a data matrix given supervised class informationUp-to-datehttps://github.com/fabriziocosta/GraphEmbedStatistics, Graphicsgraphembediuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/
graphlan1.1.3graphlanTo updategraphlanGraPhlAnPhylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classificationMetagenomics, Phylogenetics, Phylogenomics, CladisticsGraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic treesGraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.To updatehttps://github.com/biobakery/graphlanMetagenomics, Graphics, Phylogeneticsgraphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/
gtdbtk2.3.22.3.2gtdbtkUp-to-dateGTDB-TkGTDB-TkGenome alignment, Taxonomic classification, Sequence assembly, Query and retrievalMetagenomics, Taxonomy, Phylogenetics, Database management, ProteinsGTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes.a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).Up-to-datehttps://github.com/Ecogenomics/GTDBTkMetagenomicsgtdbtkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk
gtfToBed12357447ucsc-gtftogenepredTo updateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysisConvert GTF files to BED12 formatUtilities for handling sequences and assemblies from the UCSC Genome Browser project.To updatehttp://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/READMEConvert Formatsgtftobed12iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12
gubbins3.2.13.3.3gubbinsTo updategubbinsGubbinsGenotyping, Phylogenetic inference, Ancestral reconstructionPhylogeny, Genotype and phenotype, Whole genome sequencingGubbins - bacterial recombination detectionGubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.To updateSequence Analysisgubbinsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins
gvcftools0.10.17.0gvcftoolsTo updateTo updatehttps://github.com/sequencing/gvcftoolsVariant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools
gwastools0.1.01.48.0bioconductor-gwastoolsTo updategwastoolsGWASToolsDeposition, Analysis, AnnotationGWAS studyClasses for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.To updatehttps://bioconductor.org/packages/release/bioc/html/GWASTools.htmlVisualization, Variant Analysisiuc
hamronization1.0.31.1.4hamronizationTo updatehamronizationhAMRonizationData handling, Antimicrobial resistance prediction, ParsingPublic health and epidemiology, Microbiology, BioinformaticsConvert AMR gene detection tool output to hAMRonization specification format.Parse multiple Antimicrobial Resistance Analysis Reports into a common data structureTo updatehttps://github.com/pha4ge/hAMRonizationSequence Analysishamronizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization
hansel2.6.12.6.1bio_hanselUp-to-dateBiohanselBioHanselGenotyping, SNP detection, Genome assemblyWhole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural scienceHeidelberg and Enteritidis SNP ElucidationBioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.Up-to-datehttps://github.com/phac-nml/bio_hanselSequence Analysisbio_hanseliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel
hapcut21.3.31.3.3hapcut2Up-to-datehapcut2HapCUT2Haplotype mapping, Variant classificationRobust and accurate haplotype assembly for diverse sequencing technologiesHapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.mdUp-to-datehttps://github.com/vibansal/HapCUT2Assemblyhapcut2galaxy-australiahttps://github.com/galaxyproject/tools-iuc
hapog1.3.71.3.7hapogUp-to-datehapogHapo-GGenome assembly, Optimisation and refinementSequence assembly, GenomicsHapo-G - Haplotype-Aware Polishing of GenomesHapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.Up-to-datehttps://github.com/institut-de-genomique/HAPO-GAssemblyhapogiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog
happy0.3.140.3.15hap.pyTo updatehap.pyhap.pyVariant calling, Sequence analysis, GenotypingGenomics, DNA polymorphismA tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.To updatehttps://github.com/Illumina/hap.pyVariant Analysishappyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/happy
heatmap23.1.3.12.17.0r-gplotsTo updateheatmap.2 function from the R gplots packageTo updatehttps://github.com/cran/gplotsVisualizationggplot2_heatmap2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2
heinz1.01.62.0bioconductor-bionetTo updatebionetBioNetProtein interaction analysisMolecular interactions, pathways and networks, Protein interactionsAn algorithm for identification of the optimal scoring subnetwork.This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.To updatehttps://github.com/ls-cwi/heinzTranscriptomics, Visualization, Statisticsheinziuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz
hicexplorer3.7.23.7.3hicexplorerTo updateHiCExplorer: Set of programs to process, analyze and visualize Hi-C data.To updatehttps://github.com/deeptools/HiCExplorerSequence Analysis, Visualizationhicexplorerbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer
hicstuff3.1.53.2.2hicstuffTo updateTo updatehttps://github.com/koszullab/hicstuffSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff
hifiasm_meta0.3.1hamtv0.3.1hifiasm_metaTo updatehifiasm-metaHifiasm-metaSequence assemblySequence assembly, MetagenomicsA hifiasm fork for metagenome assembly using Hifi reads.Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.To updatehttps://github.com/xfengnefx/hifiasm-metaMetagenomicshifiasm_metagalaxy-australiahttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta
hisat22.2.12.2.1hisat2Up-to-datehisat2HISAT2Sequence alignmentRNA-seqHISAT2 is a fast and sensitive spliced alignment program.Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).Up-to-datehttp://ccb.jhu.edu/software/hisat2/Assemblyhisat2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2
hivclustering1.3.11.6.8python-hivclusteringTo updateInfers transmission networks from pairwise distances inferred by tn93To updatehttps://pypi.org/project/hivclustering/Next Gen Mappershivclusteringiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/
hmmer33.43.4hmmerUp-to-datehmmer3HMMER3Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database searchSequence analysis, Sequence sites, features and motifs, Gene and protein familiesHMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.Up-to-datehttp://hmmer.org/Sequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3
homer4.114.11homerUp-to-datehomerhomerSequence motif discoveryHOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.Up-to-datehttp://homer.ucsd.edu/homer/index.htmlSequence Analysisdata_manager_homer_preparseiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/homer
htseq_count2.0.52.0.5htseqUp-to-datehtseqHTSeqNucleic acid sequence analysisSequence analysisCount aligned reads (SAM/BAM) that overlap genomic features (GFF)Python framework to process and analyse high-throughput sequencing (HTS) dataUp-to-datehttps://readthedocs.org/projects/htseq/Genomic Interval Operations, SAM, Sequence Analysis, RNAhtseq_countlparsonshttps://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count
humann3.83.8humannUp-to-datehumannhumannSpecies frequency estimation, Taxonomic classification, Phylogenetic analysisMetagenomics, PhylogenomicsHUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolutionHUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”Up-to-datehttp://huttenhower.sph.harvard.edu/humannMetagenomicshumanniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/humann
hybpiper2.1.62.1.6hybpiperUp-to-dateHybPiperHybPiperSequence trimming, Sequence assembly, Read mappingPhylogenetics, Plant biology, Gene transcripts, Sequence assembly, PhylogenomicsAnalyse targeted sequence capture dataParalogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.Up-to-datehttps://github.com/mossmatters/HybPiperSequence Analysis, Phylogeneticshybpiperiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper
hyphy2.5.472.5.59hyphyTo updateHyPhyHyPhyStatistical calculationPhylogeny, Small molecules, Molecular interactions, pathways and networksHypothesis Testing using PhylogeniesSoftware package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.To updatehttp://www.hyphy.orgPhylogeneticsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/
hypo1.0.31.0.3hypoUp-to-dateHyPoHyPoOptimisation and refinement, Genome assemblySequence assembly, GenomicsSuper Fast & Accurate Polisher for Long Read Genome AssembliesHyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.Up-to-datehttps://github.com/kensung-lab/hypoAssemblyhypoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo
icescreen1.3.11.3.2icescreenTo updateicescreenICEscreenDatabase search, Protein feature detectionMobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variationICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.To updatehttps://icescreen.migale.inrae.fr/Genome annotationicescreeniuchttps://forgemia.inra.fr/ices_imes_analysis/icescreen
idba_ud1.1.3idbaTo updateidbaIDBASequence assemblySequence assemblyWrappers for the idba assembler variants.A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.To updatehttps://i.cs.hku.hk/~alse/hkubrg/projects/index.htmlAssemblyidbaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud
idr2.0.32.0.4.2idrTo updateGalaxy wrappers for the IDR package from Nathan BoleuTo updatehttps://github.com/nboley/idrSequence Analysisidriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/
idr_download0.44.15.11.1omero-pyTo updateImage Data Resource downloading toolTo updatehttps://idr.openmicroscopy.orgData Sourceidr_download_by_idsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download
iedb_api2.15.2pythonTo updateGet epitope binding predictions from IEDB-APITo updatehttp://tools.immuneepitope.org/main/tools-api/Data Source, Sequence Analysisiedb_apiiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api
instrain1.5.31.8.0instrainTo updateinstrainInStrainSNP detection, Genome comparisonMapping, MetagenomicsInStrain is a tool for analysis of co-occurring genome populations from metagenomesInStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identificationTo updatehttps://instrain.readthedocs.io/en/latest/#Metagenomicsinstrainiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain
integron_finder2.0.32.0.3integron_finderUp-to-dateintegron_finderIntegron FinderNucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotationFunctional genomics, Mobile genetic elements, Molecular biology, Sequence analysis"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"A tool to detect Integron in DNA sequences.Up-to-datehttps://github.com/gem-pasteur/Integron_FinderSequence Analysisintegronfinderiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder
intermine_galaxy_exchange0.0.18.25coreutilsTo updateInterMine ExporterTo updateConvert Formatsintermine_galaxy_exchangeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange
interproscan5.59-91.0interproscanTo updateinterproscan_ebiInterProScan (EBI)Sequence motif recognition, Protein feature detectionGene and protein families, Sequence analysisInterproscan queries the interpro database and provides annotations.Scan sequences against the InterPro protein signature databases.To updatehttp://www.ebi.ac.uk/Tools/pfa/iprscan5/Sequence Analysisinterproscanbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan
interval2maf1.0.1+galaxy10.11.0bx-pythonTo updatebx-pythonbx-pythonSequence analysisExtract MAF blocks given a set of intervalsTools for manipulating biological data, particularly multiple sequence alignments.To updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/Genomic Interval Operationsinterval2mafiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/
intervene0.6.50.6.5interveneUp-to-dateinterveneInterveneSequence comparison, Sequence visualisationComputational biologyCreate pairwise and upset plotsTool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.Up-to-datehttps://intervene.readthedocs.ioStatisticsinterveneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene
iqtree2.1.22.2.6iqtreeTo updateEfficient phylogenomic software by maximum likelihoodTo updatehttp://www.iqtree.org/Phylogeneticsiqtreeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/
irissv1.0.41.19.2samtoolsTo updateRefine insertion sequencesTo updatehttps://github.com/mkirsche/IrisVariant Analysisirissviuchttps://github.com/galaxyproject/tools-iuc/tools/irissv/
isescan1.7.2.31.7.2.1isescanTo updateISEScanISEScanStructural variation detectionGenomics, DNA structural variation, Sequence analysis, Genetic variation"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."Automated identification of insertion sequence elements in prokaryotic genomes.To updatehttps://github.com/xiezhq/ISEScanSequence AnalysisISEScaniuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan
isoformswitchanalyzer1.20.02.2.0bioconductor-isoformswitchanalyzerTo updateIsoformSwitchAnalyzeRIsoformSwitchAnalyzeRSequence comparison, Sequence analysisComputational biology, Gene transcriptsStatistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.To updatehttps://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.htmlTranscriptomics, RNA, Statisticsisoformswitchanalyzeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer
ivar1.4.21.4.2ivarUp-to-dateiVar is a computational package that contains functions broadly useful for viral amplicon-based sequencingUp-to-datehttps://github.com/andersen-lab/ivarSequence Analysisivariuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/
iwtomics1.0.01.26.0bioconductor-iwtomicsTo updateiwtomicsIWTomicsDifferential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, ComparisonStatistics and probabilityInterval-Wise Testing for Omics DataImplementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.To updatehttps://bioconductor.org/packages/release/bioc/html/IWTomics.htmlStatisticsiwtomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics
jasminesv1.0.111.1.5jasminesvTo updateMerge structural variants across samplesTo updatehttps://github.com/mkirsche/Jasmine/Variant Analysisjasminesviuchttps://github.com/galaxyproject/tools-iuc/jasminesv/
jbrowse1.16.111.16.11jbrowseUp-to-datejbrowseJBrowseGenome visualisationGenomicsJBrowse Genome Browser integrated as a Galaxy ToolSlick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.Up-to-datehttps://jbrowse.orgSequence Analysisjbrowseiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
jcvi_gff_stats0.8.41.3.9jcviTo updateCompute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)To updatehttps://github.com/tanghaibao/jcviSequence Analysisjcvi_gff_statsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats
jellyfish2.3.1kmer-jellyfishTo updateJellyfishJellyfishk-mer countingSequence analysis, GenomicsJellyfish is a tool for fast, memory-efficient counting of k-mers in DNAA command-line algorithm for counting k-mers in DNA sequence.To updatehttps://github.com/gmarcais/JellyfishAssemblyjellyfishiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish
join_files_by_id1.01.11.6r-data.tableTo updateThis tool will join datasets according to a column with identifierTo updateText Manipulationjoin_files_by_idiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id
jq1.01.5jqTo updateJQ is a lightweight and flexible command-line JSON processorTo updatehttps://stedolan.github.io/jq/Text Manipulationjqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jq
jvarkit2020122320201223jvarkit-wgscoverageplotterUp-to-dateJvarkit : Java utilities for BioinformaticsUp-to-datehttps://lindenb.github.io/jvarkit/SAMjvarkitiuchttps://github.com/galaxyproject/iuc/tree/master/tools/jvarkit
kallisto0.48.00.50.1kallistoTo updatekallistokallistoGene expression profilingTranscriptomics, RNA-seq, Gene expressionkallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.To updatehttps://pachterlab.github.io/kallisto/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/
kc-align1.0.21.0.2kcalignUp-to-datekc-alignkc-alignMultiple sequence alignmentMappingKc-Align custom toolA fast and accurate tool for performing codon-aware multiple sequence alignmentsUp-to-datehttps://github.com/davebx/kc-alignSequence Analysiskc_aligniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align
khmer3.0.0a33.0.0a3khmerUp-to-datekhmerkhmerStandardisation and normalisation, De-novo assemblySequence assemblyIn-memory nucleotide sequence k-mer counting, filtering, graph traversal and morekhmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.Up-to-datehttps://khmer.readthedocs.org/Assembly, Next Gen Mapperskhmeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer
king2.2.72.2.7kingUp-to-dateKinship-based INference for GwasUp-to-datehttp://people.virginia.edu/~wc9c/KING/Variant Analysiskingiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/king/
kleborate2.3.22.3.2kleborateUp-to-datekleborateKleborateMultilocus sequence typing, Genome assembly, Virulence predictionPublic health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencingScreen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).Up-to-datehttps://github.com/katholt/Kleborate/wikiMetagenomicskleborateiuchttps://github.com/katholt/Kleborate
kma1.2.211.4.14kmaTo updateMap with KMATo updatehttps://bitbucket.org/genomicepidemiology/kmaNext Gen Mapperskmaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kma
kofamscan1.3.01.3.0kofamscanUp-to-dateGene function annotation tool based on KEGG Orthology and hidden Markov modelUp-to-datehttps://github.com/takaram/kofam_scanSequence Analysiskofamscaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan
kraken_biom1.2.01.2.0kraken-biomUp-to-dateCreate BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)Up-to-datehttps://github.com/smdabdoub/kraken-biomMetagenomicskraken_biomiuchttps://github.com/smdabdoub/kraken-biom
kraken_taxonomy_report0.0.31.70biopythonTo updateKraken taxonomy reportTo updatehttps://github.com/blankenberg/Kraken-Taxonomy-ReportMetagenomicskraken_taxonomy_reportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report
krakentools1.21.2krakentoolsUp-to-datekrakentoolsKrakenToolsVisualisation, AggregationTaxonomy, MetagenomicsKrakenTools is a suite of scripts to be used alongside the KrakenKrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output filesUp-to-datehttps://github.com/jenniferlu717/KrakenToolsMetagenomicskrakentoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools
krocus1.0.11.0.3krocusTo updatePredict MLST directly from uncorrected long readsTo updatehttps://github.com/quadram-institute-bioscience/krocusSequence Analysiskrocusiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus
last12051542lastTo updatelastLASTSequence alignmentGenomics, Comparative genomicsLAST finds similar regions between sequences.Short read alignment program incorporating quality scoresTo updatehttp://last.cbrc.jp/Sequence Analysislastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/last
lastz1.04.221.04.22lastzUp-to-datelastzLASTZSequence alignment, Read mappingGenomicsGalaxy wrappers for the Lastz and Lastz_dA tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.Up-to-datehttps://github.com/lastz/lastzNext Gen Mapperslastzdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz
lcrgenie1.0.2lcr_genieTo updateLigase Chain Reaction GenieTo updatehttps://github.com/neilswainston/LCRGenieSynthetic Biologylcrgenieiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie
legsta0.5.10.5.1legstaUp-to-datePerforms in silico Legionella pneumophila sequence based typing.Up-to-datehttps://github.com/tseemann/legstaSequence Analysislegstaiuchttps://github.com/tseemann/legsta
length_and_gc_content0.1.21.3.2r-optparseTo updateGets gene length and gc content from a fasta and a GTF fileTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_contentFasta Manipulation, Statistics, RNA, Micro-array Analysislength_and_gc_contentiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content
limma_voom3.58.13.58.1bioconductor-limmaUp-to-datelimmalimmaRNA-Seq analysisMolecular biology, GeneticsPerform RNA-Seq differential expression analysis using limma voom pipelineData analysis, linear models and differential expression for microarray data.Up-to-datehttp://bioconductor.org/packages/release/bioc/html/limma.htmlTranscriptomics, RNA, Statisticslimma_voomiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom
lineagespot1.6.0r-baseTo updatelineagespotlineagespotVariant callingMetagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variationIdentification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).To updatehttps://www.bioconductor.org/packages/release/bioc/html/lineagespot.htmlMetagenomics, Sequence Analysislineagespotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot
links2.0.12.0.1linksUp-to-datelinksLINKSScaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimmingSequence assembly, Mapping, SequencingScaffold genome assemblies with long reads.LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.Up-to-datehttps://github.com/bcgsc/LINKSAssemblylinksiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/links
lofreq2.1.52.1.5lofreqUp-to-dateLoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.Up-to-datehttps://csb5.github.io/lofreq/Variant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq
lorikeet2020lorikeetUp-to-dateTools for M. tuberculosis DNA fingerprinting (spoligotyping)Up-to-datehttps://github.com/AbeelLab/lorikeetSequence Analysislorikeet_spoligotypeiuchttps://github.com/AbeelLab/lorikeet
lumpy_sv0.3.10.3.1lumpy-svUp-to-dateLUMPY - a general probabilistic framework for structural variant discoveryUp-to-datehttp://layerlab.org/software/Variant Analysislumpy_sviuchttps://github.com/arq5x/lumpy-sv
m6anet2.1.02.1.0m6anetUp-to-datem6Anetm6AnetQuantification, Imputation, Gene expression profilingRNA-Seq, Transcriptomics, RNA, Machine learningm6anet to detect m6A RNA modifications from nanopore dataDetection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.Up-to-datehttps://m6anet.readthedocs.io/en/latestSequence Analysism6anetiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet
maaslin20.99.120.99.12maaslin2Up-to-dateMaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.Up-to-datehttp://huttenhower.sph.harvard.edu/maaslinMetagenomicsmaaslin2iuchttps://github.com/biobakery/Maaslin2
macs22.2.9.12.2.9.1macs2Up-to-datemacsMACSPeak calling, Enrichment analysis, Gene regulatory network analysisChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sitesMACS - Model-based Analysis of ChIP-SeqModel-based Analysis of ChIP-seq data.Up-to-datehttps://github.com/taoliu/MACSSequence Analysis, Statisticsmacs2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2
maf_stats1.0.2+galaxy0To updateMAF Coverage statisticsTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/Genomic Interval Operationsmaf_statsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/
mageck0.5.9.20.5.9.5mageckTo updatemageckMAGeCKGenetic variation analysisGenetics, Genetic variation, GenomicsModel-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.To updatehttps://sourceforge.net/projects/mageck/Genome editingiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck
maker2.31.113.01.03makerTo updatemakerMAKERGenome annotationGenomics, DNA, Sequence analysisMAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.To updatehttp://www.yandell-lab.org/software/maker.htmlSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/maker
malt0.5.30.62maltTo updateAligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.To updatehttps://github.com/husonlab/maltNext Gen Mappersmalt_runiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/malt
map_param_value0.2.0To updateMap a parameter value to another valueTo updateText Manipulationmap_param_valueiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value
mapseq2.1.1perlTo updatefast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.To updatehttps://github.com/jfmrod/MAPseqMetagenomicsmapseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq
mash2.32.3mashUp-to-datemashMashSequence distance matrix generationGenomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutationFast genome and metagenome distance estimation using MinHashFast genome and metagenome distance estimation using MinHash.Up-to-datehttps://github.com/marbl/MashMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mash
mashmap3.1.33.1.3mashmapUp-to-dateFast local alignment boundariesUp-to-datehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmapSequence Analysismashmapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap
masigpro1.49.38.25coreutilsTo updatemasigpromaSigProRegression analysisGene expression, Molecular genetics, Microarray experiment, RNA-SeqIdentify significantly differential expression profiles in time-course microarray experimentsRegression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.To updatehttps://www.bioconductor.org/packages/release/bioc/html/maSigPro.htmlTranscriptomics, RNA, Statisticsmasigproiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro
maxbin22.2.7maxbin2To updatemaxbinMaxBinSequence assemblyMetagenomics, Sequence assembly, Microbiologyclusters metagenomic contigs into binsSoftware for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.To updatehttps://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.htmlMetagenomicsmaxbin2mbernthttps://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/
mcl22.28222.282mclUp-to-datemclMCLClustering, Network analysis, Gene regulatory network analysisMolecular interactions, pathways and networksThe Markov Cluster Algorithm, a cluster algorithm for graphsMCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.Up-to-datehttps://micans.org/mcl/man/mcl.htmlSequence Analysismcliuchttps://github.com/galaxyproject/tools-iuc/tree/master/mcl
medaka1.7.21.11.3medakaTo updatemedakaMedakaBase-calling, Variant calling, Sequence assemblySequence assembly, Machine learningSequence correction provided by ONT Researchmedaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.To updatehttps://github.com/nanoporetech/medakaSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka
megahit1.2.91.2.9megahitUp-to-datemegahitMEGAHITGenome assemblyMetagenomics, Sequencing, Ecology, Sequence assemblyAn ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.Up-to-datehttps://github.com/voutcn/megahitSequence Analysis, Assembly, Metagenomicsmegahitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit
megahit_contig2fastg1.1.31.2.9megahitTo updatemegahitMEGAHITGenome assemblyMetagenomics, Sequencing, Ecology, Sequence assemblyA subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.To updatehttps://github.com/voutcn/megahit/blob/master/tools/toolkit.cppSequence Analysis, Assembly, Metagenomicsmegahit_contig2fastgiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg
megan6.21.76.25.9meganTo updatemeganMEGANSequence analysis, Taxonomic classificationSequence analysisMEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.To updatehttps://github.com/husonlab/megan-ceSequence Analysismeganiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megan
meme5.4.15.5.5memeTo updatememe_fimomeme_fimoSequence motif discovery, Nucleic acid feature detection, Protein feature detection, Statistical calculationSequence analysis, Genetic variation, Statistics and probability, Data miningThe MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices.To updatehttp://meme-suite.org/ChIP-seqmemeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meme
meme_chip4.11.21.3.26graphicsmagickTo updatePerforms motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.To updatehttp://meme-suite.org/ChIP-seqmeme_chipiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip
meningotype0.8.50.8.5meningotypeUp-to-dateAssign sequence type to N. meningitidis genome assembliesUp-to-datehttps://github.com/MDU-PHL/meningotypeSequence Analysismeningotypeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype
merlin1.1.21.1.2merlinUp-to-datemerlinMerlinHaplotype mapping, Genetic mappingGWAS study, MappingPedigree Analysis packageCan be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulationUp-to-datehttp://csg.sph.umich.edu/abecasis/Merlin/Variant Analysismerliniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/
merqury1.31.3merquryUp-to-datemerquryMerquryGenome assembly, k-mer counting, Scaffolding, Phasing, De-novo assemblySequence assembly, Whole genome sequencing, Plant biologyMerqury is a tool for evaluating genomes assemblies based of k-mer operations.Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.Up-to-datehttps://github.com/marbl/merquryAssemblymerquryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury
meryl1.31.3merquryUp-to-datemerylMerylk-mer countingWhole genome sequencing, Genomics, Sequence analysis, SequencingMeryl a k-mer counter.Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.Up-to-datehttps://github.com/marbl/merylAssemblymeryliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl
metabat22.152.15metabat2Up-to-dateMetaBAT_2MetaBAT 2Read binning, Sequence assembly, Genome annotationMetagenomics, Sequence assembly, Metagenomic sequencingMetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binningUp-to-datehttps://bitbucket.org/berkeleylab/metabat/src/master/Metagenomicsmetabat2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/
metaeuk5.34c21f26.a5d39d9metaeukTo updateMetaEukMetaEukHomology-based gene predictionMetagenomics, Gene and protein familiesMetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand.MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomicsTo updatehttps://github.com/soedinglab/metaeukSequence Analysis, Genome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk
metagenomeseq1.16.0-0.0.11.43.0bioconductor-metagenomeseqTo updatemetagenomeseqmetagenomeSeqSequence visualisation, Statistical calculationMetagenomics, SequencingmetagenomeSeq NormalizationDesigned to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.To updateMetagenomicsmetagenomeseq_normalizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq
metaphlan4.0.64.1.0metaphlanTo updatemetaphlanMetaPhlAnNucleic acid sequence analysis, Phylogenetic tree analysisMetagenomics, PhylogenomicsMetaPhlAn for Metagenomic Phylogenetic AnalysisComputational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.To updatehttps://github.com/biobakery/MetaPhlAnMetagenomicsmetaphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/
migmap1.0.31.0.3migmapUp-to-dateMiGMAPMiGMAPSequence analysis, Read mappingImmunoproteins, genes and antigens, Sequence analysismapper for full-length T- and B-cell repertoire sequencingMapper for full-length T- and B-cell repertoire sequencing.Up-to-datehttps://github.com/mikessh/migmapRNA, Sequence Analysismigmapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap
minia3.2.63.2.6miniaUp-to-dateminiaMiniaGenome assemblySequence assemblyShort-read assembler based on a de Bruijn graphShort-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.Up-to-datehttps://gatb.inria.fr/software/minia/Assemblyminiaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
miniasm0.3_r1790.3miniasmTo updateMiniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)To updatehttps://github.com/lh3/miniasmAssemblyminiasmiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm
minimap22.262.26minimap2Up-to-dateminimap2Minimap2Pairwise sequence alignmentMappingA fast pairwise aligner for genomic and spliced nucleotide sequencesPairwise aligner for genomic and spliced nucleotide sequencesUp-to-datehttps://github.com/lh3/minimap2Next Gen Mappersminimap2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2
miniprot0.120.12miniprotUp-to-dateAlign a protein sequence against a genome with affine gap penalty, splicing and frameshift.Up-to-datehttps://github.com/lh3/miniprotSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot
mirnature1.11.1mirnatureUp-to-dateComputational detection of canonical microRNAsUp-to-datehttps://github.com/Bierinformatik/miRNAtureRNA, Sequence Analysismirnatureiuchttps://github.com/Bierinformatik/miRNAture
mitobim1.9.11.9.1mitobimUp-to-dateassemble mitochondrial genomesUp-to-datehttps://github.com/chrishah/MITObimAssemblymitobimiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim
mitos1.1.52.1.7mitosTo updatemitosMITOSGenome annotationZoology, Whole genome sequencingde-novo annotation of metazoan mitochondrial genomesDe novo metazoan mitochondrial genome annotation.To updatehttp://mitos.bioinf.uni-leipzig.de/Sequence Analysismitosiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos
mlst2.22.02.23.0mlstTo updatemlstMLSTTaxonomic classificationImmunoproteins, genes and antigensScan contig files against PubMLST typing schemesMulti Locus Sequence Typing from an assembled genome or from a set of reads.To updatehttps://github.com/tseemann/mlstSequence Analysismlstiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst
moabs1.3.4.61.3.9.0moabsTo updateMOABS for differential methylation analysis on Bisulfite sequencing data.To updatehttps://github.com/sunnyisgalaxy/moabsEpigeneticsmoabsiuchttps://github.com/sunnyisgalaxy/moabs
mosdepth0.3.60.3.6mosdepthUp-to-datefast and flexible BAM/CRAM depth calculationUp-to-datehttps://github.com/brentp/mosdepthSAMmosdepthiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth
mothur1.01.48.0mothurTo updatemothurmothurDNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysisMicrobial ecology, Taxonomy, Sequence analysis, PhylogenyMothur wrappersOpen-source, platform-independent, community-supported software for describing and comparing microbial communitiesTo updatehttps://www.mothur.orgMetagenomicsmothuriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur
msaboot0.1.20.1.2msabootUp-to-dateA multiple sequences alignment bootstrapping tool.Up-to-datehttps://github.com/phac-nml/msabootFasta Manipulationmsabootiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot
multigps0.74.0fonts-conda-ecosystemTo updateAnalyzes collections of multi-condition ChIP-seq data.To updatehttp://mahonylab.org/software/multigps/ChIP-seqmultigpsiuc
multigsea1.12.01.12.0bioconductor-multigseaUp-to-datemultiGSEAmultiGSEAGene-set enrichment analysis, Aggregation, Pathway analysisMetabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small moleculesGSEA-based pathway enrichment analysis for multi-omics dataA GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.Up-to-datehttps://bioconductor.org/packages/devel/bioc/html/multiGSEA.htmlTranscriptomics, Proteomics, Statisticsmultigseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea
multiqc1.111.21multiqcTo updatemultiqcMultiQCValidationSequencing, BioinformaticsMultiQC aggregates results from bioinformatics analyses across many samples into a single reportMultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.To updatehttp://multiqc.info/Fastq Manipulation, Statistics, Visualizationmultiqciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc
mummer44.0.0rc14.0.0rc1mummer4Up-to-datemumer4MUMmer4Multiple sequence alignmentSequence analysis, Human geneticsMummer4 ToolsSystem for rapidly aligning large DNA sequences to one another.Up-to-datehttps://github.com/mummer4/mummerSequence Analysismummer4iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4
mykrobe0.10.00.13.0mykrobeTo updateMykrobeMykrobeAntimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimmingWhole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, MetagenomicsAntibiotic resistance predictionsAntibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installedTo updatehttps://github.com/Mykrobe-tools/mykrobeSequence Analysismykrobeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe
mzmine3.9.03.9.0mzmineUp-to-datemzmineMZmineNatural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generationProteomics, Metabolomics, Proteomics experiment, Small moleculesmass-spectrometry data processing, with the main focus on LC-MS dataToolbox for visualization and analysis of LC-MS data in netCDF or mzXML.Up-to-datehttp://mzmine.github.io/Metabolomicsmzmine_batchiuchttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/
naltorfs0.1.20.1.2naltorfsUp-to-datenAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)Up-to-datehttps://github.com/BlankenbergLab/nAltORFsSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/
nanocompore1.0.0rc3.post21.0.4nanocomporeTo updateNanocomporeNanocomporePost-translation modification site prediction, PolyA signal detection, Genotyping, k-mer countingFunctional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sitesNanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitroTo updatehttps://nanocompore.rna.rocks/Sequence Analysisnanocomporeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore
nanoplot1.41.01.42.0nanoplotTo updatePlotting tool for long read sequencing data and alignmentsTo updatehttps://github.com/wdecoster/NanoPlotVisualizationnanoplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/
nanopolishcomp0.6.110.6.12nanopolishcompTo updateNanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.To updatehttps://a-slide.github.io/NanopolishCompSequence Analysisnanopolishcompiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp
ncbi_acc_download0.2.80.2.8ncbi-acc-downloadUp-to-dateDownload sequences from GenBank/RefSeq by accession through the NCBI ENTREZ APIUp-to-datehttps://github.com/kblin/ncbi-acc-downloadData Sourcencbi_acc_downloadiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download
ncbi_datasets15.19.1ncbi-datasets-cliTo updatencbi_datasetsNCBI DatasetsData handling, Sequence database search, Data retrievalBiological databasesNCBI datasets downloads biological sequence data across all domains of life from NCBI.NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.To updatehttps://github.com/ncbi/datasetsData Sourcencbi_datasetsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets
ncbi_entrez_direct16.216.2entrez-directUp-to-dateNCBI Entrez Direct allow fetching data from NCBI DatabasesUp-to-datehttp://www.ncbi.nlm.nih.gov/books/NBK179288/Data Sourcencbi_entrez_directiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct
ncbi_entrez_eutils1.70pythonTo updateNCBI Entrez E-Utilties allow fetching data from NCBI DatabasesTo updatehttps://www.ncbi.nlm.nih.gov/books/NBK25501/Data Sourcencbi_entrez_eutilsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils
ncbi_fcs_gx0.5.00.5.0ncbi-fcs-gxUp-to-dateFCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).Up-to-datehttps://github.com/ncbi/fcs-gxSequence Analysisncbi_fcs_gxiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx
necat0.0.1_update202008030.0.1_update20200803necatUp-to-datenecatNECATDe-novo assemblySequence assemblyError correction and de-novo assembly for ONT Nanopore readsNECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.Up-to-datehttps://github.com/xiaochuanle/NECATAssemblynecatiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/necat
newick_utils1.6+galaxy11.6newick_utilsTo updatenewick_utilitiesNewick UtilitiesPhylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstructionPhylogeny, Genomics, Computer sciencePerform operations on Newick treesThe Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.To updatehttp://cegg.unige.ch/newick_utilsVisualization, Metagenomicsnewick_utilsiuchttps://github.com/tjunier/newick_utils
nextclade2.7.02.14.0nextalignTo updateIdentify differences between your sequences and a reference sequence used by NextstrainTo updatehttps://github.com/nextstrain/nextcladeSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade
ngmlr0.2.70.2.7ngmlrUp-to-datengmlrNGMLRDNA mapping, Sequence alignment, Genetic variation analysisSequencing, Mapping, DNA structural variationCoNvex Gap-cost alignMents for Long ReadsAn algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.Up-to-datehttps://github.com/philres/ngmlrNext Gen Mappersngmlriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr
ngsutils0.5.9ngsutilsTo updatengsutilsNGSUtilsRead pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filteringGenomics, TranscriptomicsNGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.NGSUtils is a suite of software tools for working with next-generation sequencing datasetsTo updatehttps://github.com/ngsutils/ngsutilsSAMiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils
nonpareil3.1.13.4.1nonpareilTo updateEstimate average coverage in metagenomic datasetsTo updatehttp://nonpareil.readthedocs.ioMetagenomicsnonpareiliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil
novoplasty4.3.14.3.5novoplastyTo updateNOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.To updatehttps://github.com/ndierckx/NOVOPlastyAssemblynovoplastyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty
nugen_nudup2.3.32.3.3nudupUp-to-dateMarks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.Up-to-datehttp://nugentechnologies.github.io/nudup/SAM, Metagenomics, Sequence Analysis, Transcriptomicsnugen_nudupiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup
obitools1.2.131.2.13obitoolsUp-to-dateobitoolsOBIToolsSequence analysis, Sequence analysisSequence analysis, DNA, SequencingOBITools is a set of programs developed to simplify the manipulation of sequence filesSet of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.Up-to-datehttp://metabarcoding.org/obitoolsSequence Analysisobitoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools
ococo0.1.2.60.1.2.6ococoUp-to-dateVariant detection of SNVsUp-to-datehttps://github.com/karel-brinda/ococoVariant Analysisococoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo
odgi0.30.8.4odgiTo updateRepresenting large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.To updatehttps://github.com/vgteam/odgiSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/
omark0.3.0To updateProteome quality assessment softwareTo updatehttps://github.com/DessimozLab/OMArkSequence Analysisomarkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/
ont_fast5_api3.1.34.1.3ont-fast5-apiTo updateont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.To updatehttps://github.com/nanoporetech/ont_fast5_api/Nanoporeont_fast5_apiiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api
onto_toolkit1.451.45perl-onto-perlUp-to-dateONTO-Toolkit is a collection of tools for managing ontologies.Up-to-datehttp://search.cpan.org/~easr/ONTO-PERL-1.45/Ontology Manipulationonto_toolkitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit
optdoev2.0.2doebaseTo updateOptimal Design Of ExperimentTo updatehttps://github.com/pablocarb/doebaseSynthetic Biologyoptdoeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe
optitype1.3.51.3.5optitypeUp-to-datePrecision HLA typing from NGS dataUp-to-datehttps://github.com/FRED-2/OptiTypeSequence Analysisoptitypeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1
orfipy0.0.40.0.4orfipyUp-to-dateorfipyorfipyCoding region prediction, Database search, Transcriptome assembly, De-novo assemblyComputer science, RNA-Seq, Transcriptomics, Small moleculesGalaxy wrapper for ORFIPYA fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.Up-to-datehttps://github.com/urmi-21/orfipySequence Analysisorfipyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy
orthofinder2.5.52.5.5orthofinderUp-to-dateOrthoFinderOrthoFinderGenome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignmentPhylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysisAccurate inference of orthologous gene groups made easyOrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.Up-to-datehttps://github.com/davidemms/OrthoFinderPhylogenetics, Sequence Analysisorthofinderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder
packaged_annotation_loader0.1pythonTo updateTool to make cached genome annotation data available as a list of datasets collectionTo updateData Sourcepackaged_annotation_loaderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader
pangolin4.34.3pangolinUp-to-datePangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.Up-to-datehttps://github.com/cov-lineages/pangolinSequence Analysispangoliniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin
parse_mito_blast1.0.21.0.2parse_mito_blastUp-to-dateFiltering blast out from querying assembly against mitochondrial database.Up-to-datehttps://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.pySequence Analysisparse_mito_blastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast
pathview1.34.01.42.0bioconductor-pathviewTo updatepathviewpathviewPathway or network analysis, Pathway or network visualisationMolecular interactions, pathways and networks, Systems biology, Data visualisationPathview is a tool set for pathway based data integration and visualization.Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.To updatehttps://bioconductor.org/packages/release/bioc/html/pathview.htmlStatistics, RNA, Micro-array Analysispathviewiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview
pbgcpp2.0.22.0.2pbgcppUp-to-dategenomicconsensusGenomicConsensusVariant callingMappingCompute genomic consensus and call variants using PacBio reads mapped to a referenceThe GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.Up-to-datehttps://github.com/PacificBiosciences/gcppVariant Analysispbgcppiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp
pbmm21.13.11.13.1pbmm2Up-to-datepbmm2pbmm2Pairwise sequence alignment, SortingMappingA minimap2 SMRT wrapper for PacBio data.pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.Up-to-datehttps://github.com/PacificBiosciences/pbmm2Next Gen Mapperspbmm2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2
pe_histogram1.0.1openjdkTo updateContains a tool that produces an insert size histogram for a paired-end BAM file.To updatehttps://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogramGraphicspe_histogramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram
peakzilla1.0pythonTo updatePeakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.To updatehttps://github.com/steinmann/peakzillaChIP-seqpeakzillaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla
pear0.9.60.9.6pearUp-to-datepearPEARSequence mergingSequence assemblyPEAR evaluates all possible paired-end read overlapsPaired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.Up-to-datepeariuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pear
pharokka1.3.2\n pharokka\nTo update\n pharokka\nrapid standardised annotation tool for bacteriophage genomes and metagenomesTo updatehttps://github.com/gbouras13/pharokkaGenome annotationpharokkaiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
phyloseq1.38.01.46.0bioconductor-phyloseqTo updatephyloseqphyloseqDeposition, Analysis, VisualisationMicrobiology, Sequence analysis, MetagenomicsHandling and analysis of high-throughput microbiome census dataProvides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.To updatehttps://www.bioconductor.org/packages/release/bioc/html/phyloseq.htmlMetagenomicsphyloseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq
phyml3.3.202204083.3.20220408phymlUp-to-datephymlPhyMLPhylogenetic tree generation (maximum likelihood and Bayesian methods)Phylogenetics, Bioinformatics, PhylogeneticsPhyML is a phylogeny software based on the maximum-likelihood principle.Phylogenetic estimation software using Maximum LikelihoodUp-to-datehttp://www.atgc-montpellier.fr/phyml/Phylogeneticsphymliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml
picard3.1.13.1.1picardUp-to-datepicard_fastqtosampicard_fastqtosamFormattingSequencingPicard SAM/BAM manipulation tools.Create an unaligned BAM file.Up-to-datehttp://broadinstitute.github.io/picard/SAMpicarddevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/picard
pick_value0.2.0To updateCompose a text parameter value using text, integer and float valuesTo updateText Manipulationpick_valueiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value
picrust1.1.11.1.4picrustTo updatepicrustPICRUStPhylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcodingMetagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencingPICRUSt wrappersPICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.To updatehttps://picrust.github.io/picrust/Metagenomicspicrustiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust
picrust22.5.12.5.2picrust2To updatepicrust2PICRUSt2Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysisMetagenomics, Microbiology, Phylogenetics, Metagenomic sequencingPICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved StatesPICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.To updatehttps://github.com/picrust/picrust2/wikiMetagenomicspicrust2iuchttps://github.com/picrust/picrust2
pilon1.20.11.24pilonTo updatepilonpilonSequence assembly, Analysis, Read alignmentAssemblypilon is a tool for assembly improvement and variant analysis in bacteriaRead alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.To updateVariant Analysispiloniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon
pipelign0.20.2pipelignUp-to-dateMultipe sequence alignmentUp-to-datehttps://github.com/asmmhossain/pipelign/Next Gen Mapperspipeligniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign
pizzly0.37.3.10.37.3pizzlyTo updatePizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.To updatehttps://github.com/pmelsted/pizzly/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/
plasflow1.1.01.1.0plasflowUp-to-datePlasFlow - Prediction of plasmid sequences in metagenomic contigs.Up-to-datehttps://github.com/smaegol/PlasFlowSequence Analysisplasflowiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow
plasmidfinder2.1.62.1.6plasmidfinderUp-to-datePlasmidFinderPlasmidFinderGenome assembly, Scaffolding, Multilocus sequence typingWhole genome sequencing, Sequence assembly, Mapping, Probes and primers"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).Up-to-datehttps://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/Sequence Analysisplasmidfinderiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder
plink1.90b6.211.90b6.21plinkUp-to-dateplinkPLINKGenetic variation analysisGWAS studyPLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.Up-to-datehttps://www.cog-genomics.org/plinkGenome-Wide Association Studyplinkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/plink
polypolish0.5.00.6.0polypolishTo updatePolypolishPolypolishGenome assembly, Read mapping, Mapping assembly, Sequencing error detectionSequence assembly, Sequence composition, complexity and repeats, Mapping"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.To updatehttps://github.com/rrwick/PolypolishSequence Analysispolypolishiuchttps://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish
porechop0.2.4porechopTo updatePorechop - Finding and removing adapters from Oxford Nanopore readsTo updatehttps://github.com/rrwick/PorechopFasta Manipulation, Fastq Manipulationporechopiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop
poretools0.6.1a10.6.1a1poretoolsUp-to-dateporetoolsPoretoolsNucleic acid sequence analysisDNA, SequencingA flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.Up-to-datehttps://poretools.readthedocs.io/en/latest/Fasta Manipulation, Fastq Manipulationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools
presto0.6.20.7.2prestoTo updateprestopRESTONucleic acid sequence analysisSequencing, DNA, ImmunologypRESTO toolkit for immune repertoire analysis.Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.To updatehttps://presto.readthedocs.io/Sequence Analysisprestoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/presto
pretext0.0.60.0.6pretextgraphUp-to-dateProcess genome contacts maps processing images.Up-to-datehttps://github.com/wtsi-hpag/PretextSnapshotSequence Analysissuite_pretextiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext
prinseq@TOOL_VERSION+galaxy20.20.4prinseqTo updateprinseqPRINSEQRead pre-processing, Sequence trimming, Sequence contamination filteringTranscriptomics, Metagenomics, GenomicsPRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasetsPRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.To updatehttp://prinseq.sourceforge.net/manual.htmlFastq Manipulation, Metagenomicsprinseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/
progressivemauvesnapshot_2015_02_13progressivemauveTo updateMauve/ProgressiveMauve Multiple Sequence AlignerTo updateSequence Analysisprogressivemauveiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve
prokka1.14.61.14.6prokkaUp-to-dateprokkaProkkaGene prediction, Coding region prediction, Genome annotationGenomics, Model organisms, VirologyRapid annotation of prokaryotic genomesSoftware tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.Up-to-datehttp://github.com/tseemann/prokkaSequence Analysisprokkacrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/
prot-scriber0.1.40.1.5prot-scriberTo updateProtein annotation of short human readable descriptionsTo updatehttps://github.com/usadellab/prot-scriberProteomicsprot_scriberiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber
proteinortho6.3.16.3.1proteinorthoUp-to-dateproteinorthoProteinorthoHomology-based gene predictionPhylogenyProteinortho is a tool to detect orthologous proteins/genes within different species.Proteinortho is a tool to detect orthologous genes within different speciesUp-to-datehttps://gitlab.com/paulklemm_PHD/proteinorthoProteomicsproteinorthoiuchttps://gitlab.com/paulklemm_PHD/proteinortho
psiclass1.0.31.0.3psiclassUp-to-datepsiclassPsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.Up-to-datehttps://github.com/splicebox/PsiCLASSTranscriptomicspsiclassiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass
pureclip1.0.41.3.1pureclipTo updatePureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP dataTo updatehttps://github.com/skrakau/PureCLIPSequence Analysis, RNA, CLIP-seqpureclipiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip
purge_dups1.2.61.2.6purge_dupsUp-to-datepurge_dupspurge_dupsGenome assembly, Read binning, ScaffoldingSequence assemblyPurge haplotigs and overlaps in an assembly based on read depthIdentifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuencesUp-to-datehttps://github.com/dfguan/purge_dupsAssemblypurge_dupsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups
pycoqc2.5.22.5.2pycoqcUp-to-dateQC metrics for ONT BasecallingUp-to-datehttps://github.com/tleonardi/pycoQCNanoporepycoqciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc
pyega35.0.25.1.0pyega3To updateEGA python client uses the EGA REST API to download authorized datasets and files.To updatehttps://github.com/EGA-archive/ega-download-clientData Sourceega_download_clientiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3
pygenometracks3.83.8pygenometracksUp-to-datepyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.Up-to-datehttps://github.com/deeptools/pyGenomeTracksVisualizationpygenometracksiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks
pysradb1.4.22.2.0pysradbTo updatepysradbpysradbDeposition, Data retrievalSequencing, Gene transcripts, Bioinformaticspysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.To updatehttps://github.com/saketkc/pysradbSequence Analysispysradb_searchiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb
qfilt1.0.0+galaxy10.0.1qfiltTo updateFilter sequencing dataTo updatehttps://github.com/veg/qfiltFastq Manipulationqfiltiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt
qiime_add_on1.9.1qiimeTo updateQIIME to perform microbial community analysisTo updatehttp://www.qiime.orgMetagenomicsqiimeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
qiime_core1.9.1qiimeTo updateQIIME to perform microbial community analysisTo updatehttp://www.qiime.orgMetagenomicsqiimeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
qq_tools0.1.00.1.4r-qqmanTo updateTo updatehttps://CRAN.R-project.org/package=qqmanVisualization, Variant Analysisiuc
qualimap2.2.2d2.3qualimapTo updatequalimapQualiMapSequencing quality controlData quality managementPlatform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.To updatehttp://qualimap.bioinfo.cipf.es/Sequence Analysis, Transcriptomics, SAMqualimapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap
quast5.2.05.2.0quastUp-to-datequastQUASTVisualisation, Sequence assembly validationSequence assemblyQuast (Quality ASsessment Tool) evaluates genome assemblies.QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.Up-to-datehttp://quast.bioinf.spbau.ru/Assemblyquastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/quast
query_impc0.9.0requestsTo updateContains a tool to query the IMPC database.To updatehttps://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impcConvert Formats, Web Servicesquery_impciuchttps://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc
query_tabular3.3.0pythonTo updateLoads tabular files into a SQLite DB to perform a SQL query producing a tabular outputTo updateText Manipulationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular
quickmerge0.30.3quickmergeUp-to-datequickmergequickmergeGenome assembly, Scaffolding, De-novo assembly, GenotypingStructural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotypeMerge long-read and hybrid assemblies to increase contiguityQuickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.Up-to-datehttps://github.com/mahulchak/quickmergeAssemblyquickmergegalaxy-australiahttps://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge
raceid0.2.30.1.3r-raceidTo updateRaceID3, StemID2, FateID - scRNA analysisTo updatehttps://github.com/dgrun/RaceID3_StemID2_package/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3
ragtag2.1.02.1.0ragtagUp-to-dateragtagragtagGenome assemblySequence assemblyReference-guided scaffolding of draft genomes tool.RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.Up-to-datehttps://github.com/malonge/RagTagAssemblyragtagiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag
rapidnj2.3.22.3.2rapidnjUp-to-daterapidnjRapidNJPhylogenetic tree generationPhylogenyGalaxy wrapper for the RapidNJ toolA tool for fast canonical neighbor-joining tree construction.Up-to-datehttps://birc.au.dk/software/rapidnj/Phylogeneticsrapidnjiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj
rasusa0.8.00.8.0rasusaUp-to-daterasusarasusaRandomly subsample sequencing reads to a specified coverageProduces an unbiased subsample of your readsUp-to-datehttps://github.com/mbhall88/rasusaSequence Analysisrasusaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa
raven1.8.01.8.3raven-assemblerTo updateRaven is a de novo genome assembler for long uncorrected reads.To updatehttps://github.com/lbcb-sci/ravenAssemblyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raven
raxml8.2.128.2.13raxmlTo updateraxmlRAxMLSequence analysis, Phylogenetic tree analysisPhylogenetics, Sequence analysisRAxML - A Maximum Likelihood based phylogenetic inferenceA tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.To updatehttp://www.exelixis-lab.org/web/software/raxml/Phylogeneticsraxmliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml
rcorrector1.0.3+galaxy11.0.6rcorrectorTo updatercorrectorRcorrectorSequencing error detectionRNA, RNA-Seq, SequencingRcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.To updatehttps://github.com/mourisl/RcorrectorFastq Manipulationrcorrectoriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector
read_it_and_keep0.2.20.3.0read-it-and-keepTo updateRapid decontamination of SARS-CoV-2 sequencing readsTo updatehttps://github.com/GenomePathogenAnalysisService/read-it-and-keepSequence Analysisread_it_and_keepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep
recentrifuge1.14.01.14.0recentrifugeUp-to-dateRecentrifugeRecentrifugeTaxonomic classification, Expression analysis, Cross-assemblyMetagenomics, Microbial ecology, Metagenomic sequencing"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."Robust comparative analysis and contamination removal for metagenomics.Up-to-datehttps://github.com/khyox/recentrifugeMetagenomicsrecentrifugeiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge
red2018.09.102018.09.10redUp-to-dateRed (REpeat Detector)Up-to-datehttps://github.com/BioinformaticsToolsmith/RedSequence Analysisrediuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/red
repeatmasker4.1.54.1.5repeatmaskerUp-to-daterepeatmaskerRepeatMaskerGenome annotationSequence analysis, Sequence composition, complexity and repeatsRepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).Up-to-datehttp://www.repeatmasker.org/Sequence Analysisrepeat_maskerbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker
repeatmodeler2.0.5To updateRepeatModeler - Model repetitive DNATo updatehttps://www.repeatmasker.org/RepeatModeler/Genome annotationrepeatmodelercsblhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler
repmatch_gff3matplotlibTo updateContains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.To updateChIP-seqrepmatch_gff3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3
reshape21.4.2r-reshape2To updateFlexibly restructure and aggregate data using just the two functions melt and dcastTo updatehttps://cran.r-project.org/web/packages/reshape2/index.htmlText Manipulationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2
resize_coordinate_window1.0.2pythonTo updateContains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.To updateGenomic Interval Operationsresize_coordinate_windowiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window
rgcca3.0.23.0.3rgccacmdTo updatemulti-block analysisTo updatehttps://github.com/rgcca-factory/RGCCAStatisticsrgccaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca
rgrnastar2.7.11a2.7.11bstarTo updatestarSTARSequence alignmentRNA-Seq, TranscriptomicsRNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapperUltrafast universal RNA-seq data alignerTo updatehttps://github.com/alexdobin/STARNext Gen Mappers, Transcriptomicsrgrnastariuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar
ribowaltz1.2.02.0ribowaltzTo updateriboWaltzriboWaltzComputational biologyCalculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling datariboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.To updatehttps://github.com/LabTranslationalArchitectomics/riboWaltzTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz
rnaquast2.2.32.2.3rnaquastUp-to-daternaQUASTrnaQUASTDe-novo assembly, Transcriptome assembly, Sequence assembly validationSequence assembly, Transcriptomics, RNA-seqrnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.Quality assessment tool for de novo transcriptome assemblies.Up-to-datehttps://github.com/ablab/rnaquastAssembly, RNArnaquastiuchttps://git.ufz.de/lehmanju/rnaquast
roary3.13.03.13.0roaryUp-to-dateroaryRoaryGenome assemblyDNA, Genomics, MappingRoary the pangenome pipelineA high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.Up-to-datehttps://sanger-pathogens.github.io/Roary/Sequence Analysisroaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/roary
rp2biosensor3.2.1rp2biosensorTo updateBuild Sensing-Enabling Metabolic Pathways from RetroPath2.0 outputTo updatehttps://github.com/brsynth/rp2biosensorSynthetic Biologyrp2biosensoriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor
rp2paths1.5.1rp2pathsTo updateEnumerate and seperate the different pathways generated by RetroPath2.0To updatehttps://github.com/brsynth/rp2pathsSynthetic Biologyrp2pathsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths
rpbasicdesign1.2.2rpbasicdesignTo updateExtracting enzyme IDs from rpSBML filesTo updatehttps://github.com/brsynth/rpbasicdesignSynthetic Biologyrpbasicdesigniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign
rpfba5.12.3rptoolsTo updatePerform FBA for the RetroPath2.0 heterologous pathwaysTo updatehttps://github.com/brsynth/rptools/releasesSynthetic Biologyrpfbaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba
rptools5.13.1rptoolsTo updateSuite of tools that work on rpSBML formatTo updatehttps://github.com/brsynth/rptoolsSynthetic Biologyrptoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools
rrparser2.5.2rrparserTo updateReaction Rules ParserTo updatehttps://github.com/brsynth/RRParserSynthetic Biologyrrparseriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser
rseqc5.0.15.0.3rseqcTo updaterseqcRSeQCData handlingSequencingan RNA-seq quality control packageProvides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.To updatehttps://code.google.com/p/rseqc/Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualizationrseqcnileshhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc
ruvseq1.26.01.36.0bioconductor-ruvseqTo updateruvseqRUVSeqDifferential gene expression analysisGene expression, RNA-seqRemove Unwanted Variation from RNA-Seq DataThis package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.To updatehttps://www.bioconductor.org/packages/release/bioc/html/DESeq2.htmlTranscriptomics, RNA, Statisticsruvseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq
salsa22.32.3salsa2Up-to-dateSALSASALSAGenome assembly, De-novo assembly, ScaffoldingSequence assembly, DNA binding sites, MappingA tool to scaffold long read assemblies with Hi-C> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branchUp-to-datehttps://github.com/marbl/SALSAAssemblysalsaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2
samblaster0.1.240.1.26samblasterTo updatesamblasterSAMBLASTERSplit read mappingDNA, Sequencing, Mappingsamblaster marks duplicates and can output split and discordant alignments from SAM/BAM filesA tool to mark duplicates and extract discordant and split reads from SAM files.To updatehttps://github.com/GregoryFaust/samblasterSAM, Fastq Manipulation, Variant Analysissamblasteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster
sansa0.0.80.1.1sansaTo updateSansa is a tool for structural variant annotation.To updatehttps://github.com/dellytools/sansaVariant Analysissansaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa
sarscov2formatter1.01.0sarscov2formatterUp-to-datesarscov2formatter custom scriptUp-to-datehttps://github.com/nickeener/sarscov2formatterSequence Analysissarscov2formatteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter
sarscov2summary0.10.5sarscov2summaryTo updatesarscov2summary custom scriptTo updatehttps://github.com/nickeener/sarscov2summarySequence Analysissarscov2summaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary
sbml2sbol0.1.13sbml2sbolTo updateConvert SBML to SBOL formatTo updatehttps://github.com/neilswainston/SbmlToSbolSynthetic Biologysbml2sboliuc
scanpy1.9.61.7.2scanpyTo updatescanpySCANPYDifferential gene expression analysisGene expression, Cell biology, GeneticsScanpy – Single-Cell Analysis in PythonScalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.To updatehttps://scanpy.readthedocs.ioTranscriptomics, Sequence Analysisscanpyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/
scater1.22.01.30.1bioconductor-scaterTo updatescaterscaterRead pre-processing, Sequencing quality control, Sequence visualisationRNA-seq, Quality affairs, Molecular geneticsScater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.To updatehttp://bioconductor.org/packages/scater/Transcriptomics, RNA, Visualizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scater
sceasy0.0.70.0.7r-sceasyUp-to-dateConverter between difference single-cell formatsUp-to-datehttps://github.com/cellgeni/sceasy/Transcriptomicssceasy_convertiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/
schicexplorer47schicexplorerTo updatescHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.To updatehttps://github.com/joachimwolff/schicexplorerSequence Analysis, Transcriptomics, Visualizationschicexploreriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer
scikit-bio0.4.20.4.2scikit-bioUp-to-datescikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformaticsUp-to-datehttp://scikit-bio.org/Sequence Analysisscikit_bioiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio
scoary1.6.161.6.16scoaryUp-to-dateScoary calculates the assocations between all genes in the accessory genome and the traits.Up-to-datehttps://github.com/AdmiralenOla/ScoaryMetagenomicsscoaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary
scpipe1.0.0+galaxy22.2.0bioconductor-scpipeTo updatescpipescPipeGenome annotation, Validation, Alignment, VisualisationGene expression, RNA-seq, SequencingA flexible preprocessing pipeline for single-cell RNA-sequencing dataA preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.To updatehttp://bioconductor.org/packages/release/bioc/html/scPipe.htmlTranscriptomics, RNA, Statisticsscpipeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe
seacr1.31.3seacrUp-to-dateSEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.Up-to-datehttps://github.com/FredHutch/SEACREpigenetics, ChIP-seqseacriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr
selenzy_wrapper0.3.00.3.0selenzy_wrapperUp-to-datePerforms enzyme selection from a reaction query.Up-to-datehttps://github.com/brsynth/selenzy-wrapperSynthetic Biologyselenzy_wrapperiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper
semibin2.0.22.0.2semibinUp-to-datesemibinSemiBinSequence assembly, Read binningMetagenomics, Machine learning, Microbial ecology, Sequence assemblySemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural NetworksCommand tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.Up-to-datehttps://semibin.readthedocs.io/en/latest/Metagenomicssemibiniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin
seq2hla2.32.3seq2hlaUp-to-dateseq2hlaSeq2HLARead mapping, Genetic variation analysisTranscriptomics, MappingPrecision HLA typing and expression from RNAseq dataseq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.Up-to-datehttps://github.com/TRON-Bioinformatics/seq2HLASequence Analysisseq2hlaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla
seqcomplexity0.1.20.1.2seqcomplexityUp-to-dateSequence complexity for raw readsUp-to-datehttps://github.com/stevenweaver/seqcomplexitySequence Analysisiuchttps://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/
seqkit2.3.12.7.0seqkitTo updateseqkitseqkitDNA transcription, Sequence trimming, DNA translation, Sequence conversionDatabase management, Sequence analysisA cross-platform and ultrafast toolkit for FASTA/Q file manipulationFASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.To updatehttps://bioinf.shenwei.me/seqkit/Sequence Analysisseqkitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit
seqprep1.3.21.3.2seqprepUp-to-dateseqprepSeqPrepNucleic acid designGenomics, Sequence assembly, Sequencing, Probes and primersTool for merging paired-end Illumina reads and trimming adapters.Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.Up-to-datehttps://github.com/jstjohn/SeqPrepFastq Manipulation, Sequence Analysisseqprepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
seqsero21.2.11.2.1seqsero2Up-to-dateSalmonella serotype prediction from genome sequencing dataUp-to-datehttps://github.com/denglab/SeqSero2Sequence Analysisseqsero2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2
seqtk1.41.4seqtkUp-to-dateseqtkseqtkData handling, Sequence file editingData managementToolkit for processing sequences in FASTA/Q formatsA tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.Up-to-datehttps://github.com/lh3/seqtkSequence Analysisseqtkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk
seqwish0.7.50.7.9seqwishTo updateAlignment to variation graph inducerTo updatehttps://github.com/ekg/seqwishSequence Analysis, Variant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/
seurat4.3.0.13.0.2r-seuratTo updateA toolkit for quality control, analysis, and exploration of single cell RNA sequencing dataTo updatehttps://github.com/satijalab/seuratTranscriptomics, RNA, Statisticsseuratiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat
shasta0.6.00.11.1shastaTo updateFast de novo assembly of long read sequencing dataTo updatehttps://github.com/chanzuckerberg/shastaAssembly, Nanoporeshastaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta
shorah1.1.31.99.2shorahTo updateshorahShoRAHHaplotype mapping, Variant callingMetagenomics, Sequencing, GeneticsReconstruct haplotypes using ShoRAH in amplicon modeInference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.To updatehttps://github.com/cbg-ethz/shorah/blob/master/README.mdSequence Analysisshorah_ampliconiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah
shovill1.1.01.1.0shovillUp-to-dateshovillshovillGenome assemblyGenomics, Microbiology, Sequence assemblyFaster de novo assembly pipeline based around SpadesShovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.Up-to-datehttps://github.com/tseemann/shovillAssemblyshovilliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill
sickle1.33.21.33sickle-trimTo updatesicklesickleSequence trimmingData quality managementA windowed adaptive trimming tool for FASTQ files using qualityA tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.To updatehttps://github.com/najoshi/sickleFastq Manipulation, Sequence Analysissickleiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle
simtext0.0.21.0.1r-argparseTo updateA text mining framework for interactive analysis and visualization of similarities among biomedical entities.To updatehttps://github.com/dlal-group/simtextText Manipulationsimtextiuchttps://github.com/galaxyproject/tools-iuc/tools/simtext
sina1.7.21.7.2sinaUp-to-datesinaSINASequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignmentSequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, TaxonomySINA reference based multiple sequence alignmentAligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignmentUp-to-datehttps://sina.readthedocs.io/en/latest/Sequence Analysissinaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sina
sinto0.9.00.10.0sintoTo updateSinto single-cell analysis toolsTo updatehttps://github.com/timoast/sintoSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto
slamdunk0.4.30.4.3slamdunkUp-to-dateSlamdunk maps and quantifies SLAMseq readsUp-to-datehttp://t-neumann.github.io/slamdunkRNA, Transcriptomics, Sequence Analysis, Next Gen Mappersslamdunkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk
sleuth0.30.10.30.1r-sleuthUp-to-datesleuthsleuthExpression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculationRNA-seq, Gene expression, Statistics and probabilitySleuth is a program for differential analysis of RNA-Seq data.A statistical model and software application for RNA-seq differential expression analysis.Up-to-datehttps://github.com/pachterlab/sleuthTranscriptomics, RNA, Statisticssleuthiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth
smallgenomeutilities0.4.00.4.0smallgenomeutilitiesUp-to-datev-pipeV-pipeRead pre-processing, Sequence alignment, Genetic variation analysisGenomics, Population genetics, Workflows, Virology, SequencingSet of utilities for manipulating small viral genome data.Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.Up-to-datehttps://github.com/cbg-ethz/smallgenomeutilitiesSequence Analysissmallgenomeutilitiesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities
smudgeplot0.2.50.2.5smudgeplotUp-to-datesmudgeplotsSmudgeplotsSequence trimming, Genotyping, k-mer countingSequence assembly, Genetic variation, MathematicsInference of ploidy and heterozygosity structure using whole genome sequencingReference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568Up-to-datehttps://github.com/KamilSJaron/smudgeplotAssemblysmudgeplotgalaxy-australiahttps://github.com/galaxyproject/tools-iuc
snap2013_11_292013_11_29snapUp-to-datesnapSNAPGene predictionDNA, DNA polymorphism, GeneticsSNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.Up-to-datehttps://github.com/KorfLab/SNAPSequence Analysissnapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snap
sniffles1.0.122.2snifflesTo updatesnifflesSnifflesSequence analysis, Structural variation detectionDNA structural variation, SequencingGalaxy wrapper for snifflesAn algorithm for structural variation detection from third generation sequencing alignment.To updatehttps://github.com/fritzsedlazeck/SnifflesSequence Analysissnifflesiuchttps://github.com/galaxyproject/tools-iuc
snipit1.21.2snipitUp-to-datesnipitsnipitBase position variability plottingVirologySummarise snps relative to a reference sequenceSummarise snps relative to a reference sequenceUp-to-datehttps://github.com/aineniamh/snipitVariant Analysis, Sequence Analysissnipitiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit
snippy4.6.0snippyTo updatesnippysnippyPhylogenetic tree visualisation, Phylogenetic tree generation, Variant callingGenomics, Model organisms, DNA polymorphism, PhylogeneticsContains the snippy tool for characterising microbial snpsRapid haploid variant calling and core SNP phylogeny generation.To updatehttps://github.com/tseemann/snippySequence Analysissnippyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy
snp-dists0.8.20.8.2snp-distsUp-to-dateCompute pairwise SNP distance matrix from a FASTA sequence alignmentUp-to-datehttps://github.com/tseemann/snp-distsVariant Analysissnp_distsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists
snp-sites2.5.12.5.1snp-sitesUp-to-dateFinds SNP sites from a multi-FASTA alignment fileUp-to-datehttps://github.com/sanger-pathogens/snp-sitesVariant Analysissnp_sitesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites
snpeff-covid19To updatesnpeffsnpEffSNP detectionDNA polymorphism, Genetic variation, Nucleic acid sites, features and motifsSnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolboxVariant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).To updatehttp://snpeff.sourceforge.net/Genome-Wide Association Study, Variant Analysissnpeff_sars_cov_2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff
snpfreqplot1.0r-baseTo updateGenerates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 dataTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/Variant Analysissnpfreqplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/
socru2.1.72.2.4socruTo updateOrder and orientation of complete bacterial genomesTo updatehttps://github.com/quadram-institute-bioscience/socruSequence Analysissocruiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/socru
sonneityping2021020120210201sonneitypingUp-to-dateScripts for parsing Mykrobe predict results for Shigella sonnei.Up-to-datehttps://github.com/katholt/sonneitypingSequence Analysissonneitypingiuchttps://github.com/katholt/sonneityping
spades3.15.53.15.5spadesUp-to-datebiosyntheticspadesbiosyntheticSPAdesSequence assemblySequence assembly, Sequence sites, features and motifs, Genetic engineeringSPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.biosyntheticSPAdes - biosynthetic gene cluster assembly with paired-end readsUp-to-datehttps://github.com/ablab/spadesAssembly, RNA, Metagenomicsspadesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/spades
spaln2.4.9pythonTo updateSpaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.To updatehttp://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/Sequence Analysis, Genome annotationspalniuchttps://github.com/ogotoh/spaln
spotyping2.12.1spotypingUp-to-datespotypingSpoTypingVariant pattern analysisMicrobiology, Sequencing, Sequence composition, complexity and repeats, Genetic variationSpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence readsFast and accurate in silico Mycobacterium spoligotyping from sequence reads.Up-to-datehttps://github.com/xiaeryu/SpoTyping-v2.0Sequence Analysisspotypingiuchttps://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
spyboat0.1.2spyboatTo updateWavelet analysis for 3d-image stacksTo updatehttp://github.com/tensionhead/spyboatImaging, Graphicsspyboatiuchttps://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat
sra-tools3.0.83.0.10sra-toolsTo updatesra-toolsSRA Software ToolkitData handlingDNA, Genomics, SequencingNCBI Sequence Read Archive toolkit utilitiesThe SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.To updatehttps://github.com/ncbi/sra-toolsData Source, Fastq Manipulationsra_toolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools
srst20.2.01.19.2samtoolsTo updateSRST2 Short Read Sequence Typing for Bacterial PathogensTo updatehttp://katholt.github.io/srst2/Metagenomicssrst2iuchttps://github.com/katholt/srst2
stacks2.65stacksTo updatestacksStacksData handlingMapping, Population geneticsStacks is a software pipeline for building loci from short-read sequences, such as RAD-seqDeveloped to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.To updatehttp://catchenlab.life.illinois.edu/stacks/Sequence Analysisstacksiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks
stacks22.552.65stacksTo updateStacks is a software pipeline for building loci from short-read sequences, such as RAD-seqTo updatehttp://catchenlab.life.illinois.edu/stacks/Sequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2
star_fusion0.5.4-3+galaxy11.12.0star-fusionTo updateSTAR Fusion detects fusion genes in RNA-Seq data after running RNA-STARTo updateSequence Analysis, Transcriptomicsstar_fusioniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion
straindesign3.2.23.2.2straindesignUp-to-dateToolbox to optimize biological modelUp-to-datehttps://github.com/brsynth/straindesignSystems Biology, Synthetic Biologystraindesigniuchttps://github.com/brsynth/straindesign
strelka2.9.102.9.10strelkaUp-to-dateUp-to-datehttps://github.com/Illumina/strelka/Variant Analysisstrelkaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka
stringtie2.2.12.2.1stringtieUp-to-datestringtieStringTieTranscriptome assembly, RNA-Seq analysisTranscriptomics, RNA-seqStringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.Up-to-datehttp://ccb.jhu.edu/software/stringtie/Transcriptomicsstringtieiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie
structure2.3.42.3.4structureUp-to-datestructureStructureGenetic variation analysisPopulation geneticsfor using multi-locus genotype data to investigate population structure.The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.Up-to-datePhylogenetics, Variant Analysisstructureiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/structure
structureharvester0.6.940.6.94structureharvesterUp-to-datefor parsing STRUCTURE outputs and for performing the Evanno methodUp-to-datePhylogenetics, Variant Analysisstructureharvesteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester
swift1.01.0swiftlinkUp-to-dateParallel MCMC Linkage AnalysisUp-to-datehttps://github.com/ajm/swiftlinkVariant Analysisswiftlinkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/
syndiva1.0clustaloTo updateSynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.To updateProteomicssyndivaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA
table_compute1.2.4pandasTo updatePerform general-purpose table operationsTo updateText Manipulationtable_computeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute
tag_pileup_frequency1.0.2openjdkTo updateContains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.To updatehttps://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileupStatistics, SAM, Genomic Interval Operationstag_pileup_frequencyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency
tasmanian_mismatch1.0.71.0.7tasmanian-mismatchUp-to-dateAnalysis of positional mismatchesUp-to-dateSequence Analysistasmanian_mismatchiuchttps://github.com/nebiolabs/tasmanian-mismatch
taxonomy_filter_refseq0.3.01.0.7rust-ncbitaxonomyTo updateFilter RefSeq by taxonomyTo updatehttps://github.com/pvanheus/ncbitaxonomySequence Analysis, Genome annotationtaxonomy_filter_refseqiuchttps://github.com/galaxyproject/tools-iuc
taxonomy_krona_chart2.7.1+galaxy02.8.1kronaTo updatekronaKronaVisualisationMetagenomicsKrona pie chart from taxonomic profileKrona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).To updatehttp://sourceforge.net/projects/krona/Assemblytaxonomy_krona_chartcrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart
tb-profiler4.4.15.0.1tb-profilerTo updateProcesses M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.To updatehttps://github.com/jodyphelan/TBProfilerSequence Analysistbprofileriuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler
tb_variant_filter0.4.00.4.0tb_variant_filterUp-to-dateM. tuberculosis H37Rv VCF filterUp-to-datehttps://github.com/COMBAT-TB/tb_variant_filterVariant Analysistb_variant_filteriuchttps://github.com/COMBAT-TB/tb_variant_filter
tbl2gff31.20.6.6bcbiogffTo updateTable to GFF3To updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3Convert Formats, Sequence Analysistbl2gff3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3
tbvcfreport0.1.100.1.10tbvcfreportUp-to-dateGenerate HTML report from SnpEff M.tuberculosis VCF(s)Up-to-datehttps://github.com/COMBAT-TB/tbvcfreportVariant Analysistbvcfreportiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport
te_finder1.0.11.19.2samtoolsTo updatetefinderTEfinderGenome indexing, Variant calling, PCR primer designSequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variationTransposable element insertions finderA Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.To updatehttps://github.com/VistaSohrab/TEfinderSequence Analysiste_finderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/
telescope1.0.31.0.3telescopeUp-to-dateTelescope-expressionTelescopeEssential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mappingRNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assemblySingle locus resolution of Transposable ELEment expression.Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.Up-to-datehttps://github.com/mlbendall/telescope/Genome annotationtelescope_assigniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope
tetoolkit2.2.32.2.3tetranscriptsUp-to-dateThe TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.Up-to-datehttp://hammelllab.labsites.cshl.edu/software/Sequence Analysistetoolkitiuchttps://github.com/mhammell-laboratory/TEtranscripts
tetyper1.11.1tetyperUp-to-dateType a specific transposable element (TE) of interest from paired-end sequencing data.Up-to-datehttps://github.com/aesheppard/TETyperSequence Analysistetyperiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper
tn931.0.61.0.13tn93To updateCompute distances between sequencesTo updatehttps://github.com/veg/tn93/Sequence Analysistn93iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/
tracy0.6.10.7.6tracyTo updateTo updateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy
transdecoder5.5.05.7.1transdecoderTo updateTransDecoderTransDecoderCoding region prediction, de Novo sequencing, De-novo assemblyGenomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencingTransDecoder finds coding regions within transcriptsTransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.To updatehttps://transdecoder.github.io/Transcriptomics, RNAtransdecoderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder
transit3.0.23.2.3transitTo updatetransitTRANSITTransposon predictionDNA, Sequencing, Mobile genetic elementsTRANSITA tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.To updatehttps://github.com/mad-lab/transit/Genome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/
transtermhp2.09transtermhpTo updateFinds rho-independent transcription terminators in bacterial genomesTo updateSequence Analysistranstermhpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp
trimmomatic0.390.39trimmomaticUp-to-dateA flexible read trimming tool for Illumina NGS dataUp-to-datehttp://www.usadellab.org/cms/?page=trimmomaticFastq Manipulationtrimmomaticpjbriggshttps://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic
trinity2.15.12.15.1trinityUp-to-datetrinityTrinityTranscriptome assemblyTranscriptomics, Gene expression, Gene transcriptsTrinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseqTrinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.Up-to-datehttps://github.com/trinityrnaseq/trinityrnaseqTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity
trinotate3.2.24.0.2trinotateTo updatetrinotateTrinotateGene functional annotationGene expression, TranscriptomicsTrinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.To updatehttps://trinotate.github.io/Transcriptomics, RNAtrinotateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate
trycycler0.5.40.5.4trycyclerUp-to-dateTrycycler toolkit wrappersUp-to-datehttps://github.com/rrwick/TrycyclerAssemblytrycycleriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler
tsebra1.1.2.31.1.2.3tsebraUp-to-dateThis tool has been developed to combine BRAKER predictions.Up-to-datehttps://github.com/Gaius-Augustus/TSEBRAGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra
tsne0.0.20.13r-rtsneTo updateT-Distributed Stochastic Neighbor Embedding using a Barnes-Hut ImplementationTo updatehttps://cran.r-project.org/web/packages/Rtsne/Text Manipulationtsneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne
tximport1.22.01.30.0bioconductor-tximportTo updatetximporttximportPathway or network analysis, Formatting, RNA-Seq analysisTranscriptomics, Gene transcripts, WorkflowsWrapper for the Bioconductor package tximportAn R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.To updatehttp://bioconductor.org/packages/tximport/Transcriptomicstximportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport
ucsc_blat377445ucsc-blatTo updateblatBLATSequence alignmentSequence analysisStandalone blat sequence search command line toolFast, accurate spliced alignment of DNA sequences.To updatehttp://genome.ucsc.edu/goldenPath/help/blatSpec.htmlSequence Analysisucsc_blatyating-l
fasplit377377ucsc-fasplitUp-to-dateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysisfaSplit is a tool to split a single FASTA file into several filesUtilities for handling sequences and assemblies from the UCSC Genome Browser project.Up-to-datehttp://hgdownload.cse.ucsc.edu/admin/exe/Fasta Manipulationucsc_fasplitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit
fatovcf448448ucsc-fatovcfUp-to-dateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysisConvert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffsUtilities for handling sequences and assemblies from the UCSC Genome Browser project.Up-to-datehttp://hgdownload.cse.ucsc.edu/admin/exe/Convert Formatsucsc_fatovcfiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf
twobittofa377455ucsc-twobittofaTo updateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysistwoBitToFa is a tool to convert all or part of .2bit file to FASTAUtilities for handling sequences and assemblies from the UCSC Genome Browser project.To updatehttps://genome.ucsc.edu/goldenpath/help/twoBit.htmlConvert Formatsucsc_twobittofaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa
wigtobigwig447447ucsc-wigtobigwigUp-to-dateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysisconverts bedGraph (wig) files into binary bigwigUtilities for handling sequences and assemblies from the UCSC Genome Browser project.Up-to-datehttps://genome.ucsc.edu/goldenPath/help/bigWig.htmlConvert Formatsucsc_wigtobigwigiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig
umi_tools1.1.21.1.5umi_toolsTo updateumi-toolsUMI-toolsSequencing quality controlNGS, Sequence sites, features and motifs, Quality affairsUMI-tools extract - Extract UMIs from fastqTools for handling Unique Molecular Identifiers in NGS data sets.To updatehttps://github.com/CGATOxford/UMI-toolsSequence Analysis, Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools
unicycler0.5.00.5.0unicyclerUp-to-dateunicyclerUnicyclerGenome assembly, AggregationMicrobiology, Genomics, Sequencing, Sequence assemblyUnicycler is a hybrid assembly pipeline for bacterial genomes.A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.Up-to-datehttps://github.com/rrwick/UnicyclerAssemblyunicycleriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler
usher0.2.10.6.3usherTo updateUShER toolkit wrappersTo updatehttps://github.com/yatisht/usherPhylogeneticsusheriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/usher
valet1.0valetTo updateA pipeline for detecting mis-assemblies in metagenomic assemblies.To updatehttps://github.com/marbl/VALETMetagenomicsvaletiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/valet
vapor1.0.21.0.2vaporUp-to-datevaporVAPORData retrieval, De-novo assembly, Read mappingWhole genome sequencing, Mapping, Sequence assemblyClassify Influenza samples from raw short read sequence dataVAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.Up-to-datehttps://github.com/connor-lab/vaporSequence Analysisvaporiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor
vardict1.8.3pythonTo updateVarDict - calls SNVs and indels for tumour-normal pairsTo updatehttps://github.com/AstraZeneca-NGS/VarDictJavaVariant Analysisvardict_javaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict
variant_analyzer2.0.0matplotlibTo updateCollection of tools for analyzing variants in duplex consensus sequencing (DCS) dataTo updateVariant Analysisvariant_analyzeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer
varscan2.4.32.4.6varscanTo updateVarScan is a variant caller for high-throughput sequencing dataTo updatehttps://dkoboldt.github.io/varscan/Variant Analysisvarscaniuchttps://github.com/galaxyproject/iuc/tree/master/tools/varscan
varvamp1.1.11.1.1varvampUp-to-datevarvampvarVAMPPCR primer designVirologyVariable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse virusesvariable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.Up-to-datehttps://github.com/jonas-fuchs/varVAMP/Sequence Analysisvarvampiuchttps://github.com/jonas-fuchs/varVAMP
vcf2maf1.6.211.6.21vcf2mafUp-to-datevcf2maf: Convert VCF into MAFUp-to-dateConvert Formatsvcf2mafiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf
vcfanno0.3.50.3.5vcfannoUp-to-datevcfannovcfannoSNP annotationGenetic variation, Data submission, annotation and curationAnnotate VCF filesFast, flexible annotation of genetic variants.Up-to-datehttps://github.com/brentp/vcfannoVariant Analysisvcfannoiuchttps://github.com/galaxyproject/tools-iuc/vcfanno/
vegan2.4-32.3_4r-veganTo updateTo updatehttps://cran.r-project.org/package=veganMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/
velocyto0.17.170.17.17velocyto.pyUp-to-dateVelocyto is a library for the analysis of RNA velocity.Up-to-datehttp://velocyto.org/Transcriptomicsvelocytoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto
velvet1.2.10velvetTo updatevelvetVelvetFormatting, De-novo assemblySequence assemblyde novo genomic assembler specially designed for short read sequencing technologiesA de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.To updatehttps://www.ebi.ac.uk/~zerbino/velvet/Assemblyvelvetdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet
velvet_optimiser2.2.6+galaxy21.2.10velvetTo updatevelvetoptimiserVelvetOptimiserOptimisation and refinement, Sequence assemblyGenomics, Sequence assemblyAutomatically optimize Velvet assembliesThis tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.To updateAssemblyvelvetoptimisersimon-gladmanhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser
verkko1.3.12.0verkkoTo updateTelomere-to-telomere assembly pipelineTo updatehttps://github.com/marbl/verkkoAssemblyverkkoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko
vg1.23.01.55.0vgTo updateVariation graph data structures, interchange formats, alignment, genotyping, and variant calling methodsTo updatehttps://github.com/vgteam/vgSequence Analysis, Variant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vg
virhunter1.0.0numpyTo updatevirhunterVirHunterSequence classificationVirologyDeep Learning method for novel virus detection in sequencing dataVirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).To updatehttps://github.com/cbib/virhunterMachine Learningvirhunteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter
volcanoplot0.0.52.2.1r-ggplot2To updateTool to create a Volcano PlotTo updateVisualization, Transcriptomics, Statisticsvolcanoplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot
vsearch2.8.32.27.0vsearchTo updatevsearchVSEARCHDNA mapping, Chimera detectionMetagenomics, Sequence analysisVSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.To updatehttps://github.com/torognes/vsearchSequence Analysisvsearchiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch
vsnp3.0.60.22.0pysamTo updateThe vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.To updatehttps://github.com/USDA-VS/vSNPSequence Analysisvsnpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp
weather_app0.1.2curlTo updateprovides simple weather in text formatTo updatehttp://wttr.in/Visualization, Web Servicessimpleweatheriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app
weblogo33.5.03.7.9weblogoTo updateweblogoWebLogoSequence cluster visualisation, Sequence visualisation, Sequence motif recognitionNucleic acid sites, features and motifs, Sequence analysisSequence Logo generator for fastaWeb-based application designed to make generate sequence logos.To updateGraphicsweblogo3devteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3
windowmasker1.02.15.0blastTo updateIdentify repetitive regions using WindowMaskerTo updatehttps://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/Sequence Analysiswindowmaskeriuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/
winnowmap2.032.03winnowmapUp-to-dateA long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.Up-to-datehttps://github.com/marbl/WinnowmapNext Gen Mapperswinnowmapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap
xpath1.47perl-xml-xpathTo updateXPath XML querying toolTo updatehttp://search.cpan.org/dist/XML-XPath/Text Manipulationxpathiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath
yahs1.2a.21.2a.2yahsUp-to-dateYet Another Hi-C scaffolding toolUp-to-datehttps://github.com/c-zhou/yahsAssemblyyahsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs
zerone1.01.0zeroneUp-to-dateChIP-seq discretization and quality controlUp-to-datehttps://github.com/nanakiksc/zeroneChIP-seqzeroneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone
bamtools2.5.22.5.2bamtoolsUp-to-dateOperate on and transform BAM datasets in various ways using bamtoolsUp-to-datehttps://github.com/pezmaster31/bamtoolsSequence Analysis, SAMbamtoolsdevteamhttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
bamtools_filter2.5.22.5.2bamtoolsUp-to-dateFilter BAM datasets on various attributes using bamtools filterUp-to-datehttps://github.com/pezmaster31/bamtoolsSequence Analysis, SAMbamtools_filterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter
bamtools_split2.5.22.5.2bamtoolsUp-to-dateUp-to-datehttps://github.com/pezmaster31/bamtoolsSequence Analysis, SAMiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split
biotradis1.4.51.4.5biotradisUp-to-dateBio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.Up-to-datehttps://www.sanger.ac.uk/science/tools/bio-tradisGenome annotationbiotradisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis
cuffcompare2.2.12.2.1cufflinksUp-to-dateGalaxy wrappers for the Cuffcompare tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffcomparedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare
cuffdiff2.2.12.2.1cufflinksUp-to-dateGalaxy wrappers for the Cuffdiff tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffdiffdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff
cufflinks2.2.12.2.1cufflinksUp-to-dateGalaxy wrappers for the Cufflinks tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscufflinksdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks
cuffmerge2.2.12.2.1cufflinksUp-to-dateGalaxy wrappers for the Cuffmerge tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffmergedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge
cuffnorm2.2.12.2.1cufflinksUp-to-dateThe Cuffnorm toolUp-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffnormdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm
cuffquant2.2.12.2.1cufflinksUp-to-dateThe Cuffquant toolUp-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffquantdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant
fasta_clipping_histogram0.0.140.0.14fastx_toolkitUp-to-dateLength Distribution chartUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Graphics, Statisticsfasta_clipping_histogramdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram
fasta_formatter0.0.140.0.14fastx_toolkitUp-to-dateFASTA Width formatterUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulationfasta_formatterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter
fasta_nucleotide_changer0.0.140.0.14fastx_toolkitUp-to-dateRNA/DNA converter.Up-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulationfasta_nucleotide_changerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer
fastq_quality_boxplot0.0.140.0.14fastx_toolkitUp-to-dateDraw quality score boxplotUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulation, Graphics, Statisticsfastq_quality_boxplotdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot
fastq_quality_converter0.0.140.0.14fastx_toolkitUp-to-dateQuality format converter (ASCII-Numeric)Up-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulationfastq_quality_converterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter
fastq_quality_filter0.0.140.0.14fastx_toolkitUp-to-dateFilter by qualityUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulationfastq_quality_filterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter
fastq_to_fasta0.0.140.0.14fastx_toolkitUp-to-dateFASTQ to FASTA converterUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Convert Formatsfastq_to_fastadevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta
fastx_artifacts_filter0.0.140.0.14fastx_toolkitUp-to-dateRemove sequencing artifactsUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_artifacts_filterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter
fastx_barcode_splitter0.0.140.0.14fastx_toolkitUp-to-dateBarcode SplitterUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_barcode_splitterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter
fastx_clipper0.0.140.0.14fastx_toolkitUp-to-dateClip adapter sequencesUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_clipperdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper
fastx_collapser0.0.140.0.14fastx_toolkitUp-to-dateCollapse sequencesUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulationfastx_collapserdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser
fastx_nucleotides_distribution0.0.140.0.14fastx_toolkitUp-to-dateDraw nucleotides distribution chartUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulation, Graphicsfastx_nucleotides_distributiondevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution
fastx_quality_statistics0.0.140.0.14fastx_toolkitUp-to-dateCompute quality statisticsUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulation, Statisticsfastx_quality_statisticsdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics
fastx_renamer0.0.140.0.14fastx_toolkitUp-to-dateRename sequencesUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_renamerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer
fastx_reverse_complement0.0.140.0.14fastx_toolkitUp-to-dateReverse-ComplementUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulation, Fasta Manipulationfastx_reverse_complementdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement
fastx_trimmer0.0.140.0.14fastx_toolkitUp-to-dateTrim sequencesUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_trimmerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer
fastq_combiner1.1.51.1.5galaxy_sequence_utilsUp-to-dateCombine FASTA and QUAL into FASTQUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulation, Fasta Manipulationfastq_combinerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner
fastq_filter1.1.51.1.5galaxy_sequence_utilsUp-to-dateFilter FASTQ reads by quality score and lengthUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_filterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter
fastq_groomer1.1.51.1.5galaxy_sequence_utilsUp-to-dateConvert between various FASTQ quality formats.Up-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_groomerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer
fastq_manipulation1.1.51.1.5galaxy_sequence_utilsUp-to-dateManipulate FASTQ reads on various attributes.Up-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_manipulationdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation
fastq_masker_by_quality1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ Masker by quality scoreUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_masker_by_qualitydevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality
fastq_paired_end_deinterlacer1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ de-interlacer on paired end reads.Up-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_paired_end_deinterlacerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer
fastq_paired_end_interlacer1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ interlacer on paired end readsUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_paired_end_interlacerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer
fastq_paired_end_joiner1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ joiner on paired end readsUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_paired_end_joinerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner
fastq_paired_end_splitter1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ splitter on joined paired end readsUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_paired_end_splitterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter
fastq_stats1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ Summary Statistics by columnUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_statsdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats
fastq_to_tabular1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ to Tabular converterUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_to_tabulardevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular
fastq_trimmer1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ Trimmer by qualityUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_trimmerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer
fastqtofasta1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ to FASTA converterUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastqtofastadevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta
tabular_to_fastq1.1.51.1.5galaxy_sequence_utilsUp-to-dateTabular to FASTQ converterUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationtabular_to_fastqdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq
kraken1.1.1krakenTo updateKraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.To updatehttp://ccb.jhu.edu/software/kraken/Metagenomicskrakendevteamhttps://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/
kraken22.1.12.1.3kraken2To updatekraken2kraken2Taxonomic classificationTaxonomy, MetagenomicsKraken2 for taxonomic designation.Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.To updatehttp://ccb.jhu.edu/software/kraken/Metagenomicskraken2iuchttps://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/
samtools1.15.11.19.2samtoolsTo updateTo updatehttps://github.com/samtools/samtoolsSAMiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools
snpeff1.70biopythonTo updateSnpEff is a genetic variant annotation and effect prediction toolboxTo updatehttp://snpeff.sourceforge.net/Genome-Wide Association Study, Variant Analysissnpeffiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff
snpsift5.2snpsiftTo updatesnpEff SnpSift tools from Pablo CingolaniTo updatehttp://snpeff.sourceforge.net/SnpSift.htmlVariant Analysissnpsiftiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift
snpsift_dbnsfp5.2snpsiftTo updatesnpEff SnpSift dbnsfp tool from Pablo CingolaniTo updatehttp://snpeff.sourceforge.net/SnpSift.html#dbNSFPVariant Analysissnpsift_dbnsfpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp
snpsift_genesets5.2snpsiftTo updateAnnotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, ReactomeTo updatehttp://snpeff.sourceforge.net/SnpSift.html#geneSetsVariant Analysissnpsift_genesetsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/
vcf2tsv1.0.9vcflibTo updateConverts VCF files into tab-delimited formatTo updatehttps://github.com/ekg/vcflibVariant Analysis, Convert Formatsvcf2tsvdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv
vcfaddinfo1.0.9vcflibTo updateAdds info fields from the second dataset which are not present in the first dataset.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfaddinfodevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo
vcfallelicprimitives1.0.9vcflibTo updateSplits alleleic primitives (gaps or mismatches) into multiple VCF linesTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfallelicprimitivesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives
vcfannotate1.0.9vcflibTo updateIntersect VCF records with BED annotationsTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfannotatedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate
vcfannotategenotypes1.0.9vcflibTo updateAnnotate genotypes in a VCF dataset using genotypes from another VCF dataset.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfannotategenotypesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes
vcfbedintersect1.0.9vcflibTo updateIntersect VCF and BED datasetsTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfbedintersectdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect
vcfbreakcreatemulti1.0.9vcflibTo updateBreak multiple alleles into multiple records, or combine overallpoing alleles into a single recordTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfbreakcreatemultidevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti
vcfcheck1.0.9vcflibTo updateVerify that the reference allele matches the reference genomeTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfcheckdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck
vcfcombine1.0.9vcflibTo updateCombine multiple VCF datasetsTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfcombinedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine
vcfcommonsamples1.0.9vcflibTo updateOutput records belonging to samples commong between two datasets.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfcommonsamplesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples
vcfdistance1.0.9vcflibTo updateCalculate distance to the nearest variant.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfdistancedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance
vcffilter1.0.9vcflibTo updateTool for filtering VCF filesTo updatehttps://github.com/ekg/vcflibVariant Analysisvcffilterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter
vcffixup1.0.9vcflibTo updateCount the allele frequencies across alleles present in each record in the VCF file.To updatehttps://github.com/ekg/vcflibVariant Analysisvcffixupdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup
vcfflatten1.0.9vcflibTo updateRemoves multi-allelic sites by picking the most common alternateTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfflattendevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten
vcfgeno2haplo1.0.9vcflibTo updateConvert genotype-based phased alleles into haplotype allelesTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfgeno2haplodevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo
vcfgenotypes1.0.9vcflibTo updateConvert numerical representation of genotypes to allelic.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfgenotypesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes
vcfhethom1.0.9vcflibTo updateCount the number of heterozygotes and alleles, compute het/hom ratio.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfhethomdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom
vcfleftalign1.0.9vcflibTo updateLeft-align indels and complex variants in VCF datasetTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfleftaligndevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign
vcfprimers1.0.9vcflibTo updateExtract flanking sequences for each VCF recordTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfprimersdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers
vcfrandomsample1.0.9vcflibTo updateRandomly sample sites from VCF datasetTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfrandomsampledevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample
vcfselectsamples1.0.9vcflibTo updateSelect samples from a VCF fileTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfselectsamplesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples
vcfsort1.0.9vcflibTo updateSort VCF dataset by coordinateTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfsortdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort
vcfvcfintersect1.0.9vcflibTo updateIntersect two VCF datasetsTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfvcfintersectdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect
ThermoRawFileParser1.3.41.4.3thermorawfileparserTo updateThermo RAW file converterTo updatehttps://github.com/compomics/ThermoRawFileParserProteomicsthermo_raw_file_convertergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser
appendfdr0.2.0To updateTo updateappendfdrgalaxyp
bed_to_protein_map0.2.0pythonTo updateConverts a BED file to a tabular list of exon locationsTo updateProteomicsbed_to_protein_mapgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map
blast_plus_remote_blastp2.6.02.15.0blastTo updateNCBI BLAST+ with -remote optionTo updatehttps://blast.ncbi.nlm.nih.gov/Sequence Analysisblast_plus_remote_blastpgalaxyphttps://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
bumbershoot3.0.211423_0_21142_0e4f4a4bumbershootTo updateTo updatehttp://proteowizard.sourceforge.net/Proteomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
calisp3.0.133.0.13calispUp-to-dateCalgary approach to isotopes in proteomicsUp-to-datehttps://github.com/kinestetika/Calisp/Proteomicscalispgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/calisp
cardinal2.10.03.4.3bioconductor-cardinalTo updateStatistical and computational tools for analyzing mass spectrometry imaging datasetsTo updatehttp://cardinalmsi.orgProteomics, Metabolomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal
dbbuilder0.3.4wgetTo updateProtein Database DownloaderTo updatehttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilderProteomicsdbbuildergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder
decoyfastaTo updateGalaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.To updateProteomicsdecoyfastagalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta
dia_umpire2.1.32.1.6dia_umpireTo updateDIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomicsTo updatehttp://diaumpire.sourceforge.net/Proteomicsdia_umpiregalaxyphttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire
dialignr1.2.02.10.0bioconductor-dialignrTo updateDIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.To updatehttps://github.com/shubham1637/DIAlignRProteomicsdialignrgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr
diann1.8.1To updateDiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.To updatehttps://github.com/vdemichev/DiaNNProteomicsdianngalaxyphttps://github.com/vdemichev/DiaNN
diapysef0.3.5.01.0.10diapysefTo updatediapysef is a convenience package for working with DIA-PASEF dataTo updatehttps://pypi.org/project/diapysef/Proteomicsdiapysefgalaxyphttps://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef
diffacto1.0.61.0.6diffactoUp-to-dateDiffacto comparative protein abundance estimationUp-to-datehttps://github.com/statisticalbiotechnology/diffactoProteomicsdiffactogalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto
digestdb0.1.0trans_proteomic_pipelineTo updateTo updatedigestdbgalaxyp
directag_and_tagreconTo updateTo updatedirectag_and_tagrecongalaxyp
data_manager_eggnog_mapperTo updatedownloads eggnog data for eggnog-mapperTo updateProteomicsdata_manager_eggnog_mappergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager
data_manager_eggnog_mapper_abspathTo updatedownload eggnog data for eggnog-mapperTo updateProteomicsdata_manager_eggnog_mapper_abspathgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath
eggnog_mapper2.1.82.1.12eggnog-mapperTo updateeggnog-mapper-v2eggNOG-mapper v2Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrievalMetagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysiseggnog-mapper fast functional annotation of novel sequencesEggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.To updateProteomicseggnog_mappergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
encyclopedia1.12.342.12.30encyclopediaTo updateMass Spec Data-Independent Acquisition (DIA) MS/MS analysisTo updatehttps://bitbucket.org/searleb/encyclopedia/wiki/HomeProteomicsencyclopediagalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia
fasta_merge_files_and_filter_unique_sequences1.2.0pythonTo updateConcatenate FASTA database files togetherTo updatehttps://github.com/galaxyproteomics/tools-galaxyp/Fasta Manipulationfasta_merge_files_and_filter_unique_sequencesgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences
fastg2protlib1.0.2To updateGenerate FASTA from FASTGTo updatehttps://github.com/galaxyproteomics/fastg2protlib.gitProteomicsfastg2protlibgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib
feature_alignment0.11.00.11.0msproteomicstoolsUp-to-dateTRIC integrates information from all available runs via a graph-based alignment strategyUp-to-dateProteomicsfeature_alignmentgalaxyphttps://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md
filter_by_fasta_ids2.3pythonTo updateFilter FASTA on the headers and/or the sequencesTo updateFasta Manipulation, Proteomicsfilter_by_fasta_idsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids
flashlfq1.0.3.11.2.6flashlfqTo updateFlashLFQ mass-spectrometry proteomics label-free quantificationTo updatehttps://github.com/smith-chem-wisc/FlashLFQProteomicsflashlfqgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq
gffcompare_to_bed0.2.1pythonTo updateFilter and convert a gffCompare GTF to BEDTo updatehttps://github.com/gpertea/gffcompare/Convert Formatsgffcompare_to_bedgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed
hardklor2.30.1+galaxy12.3.2hardklorTo updateHardklörTo updateProteomicshardklorgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor
idconvert3_0_9992proteowizardTo updateConvert mass spectrometry identification files on linux or MacOSXTo updateProteomicsidconvertgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
lfq_protein_quant1.02.28.1bioconductor-msnbaseTo updateEnable protein summarisation and quantitationTo updatehttps://github.com/compomics/LFQ_galaxy_pProteomicslfq_protein_quantgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant
ltq_iquant_cliTo updateTo updateltq_iquant_cligalaxyp
maldiquant1.22.0r-baseTo updateMALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.To updatehttp://strimmerlab.org/software/maldiquant/ProteomicsMALDIquantgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant
map_peptides_to_bed0.21.70biopythonTo updateMap peptides to a reference genome for display by a genome browserTo updateProteomicsmap_peptides_to_bedgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed
maxquant2.0.3.02.0.3.0maxquantUp-to-datewrapper for MaxQuantUp-to-datehttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquantProteomicsmaxquantgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
meta_proteome_analyzer2.0.02.0.0mpa-portableUp-to-dateMetaProteomeAnalyzerUp-to-datehttps://github.com/compomics/meta-proteome-analyzer/Proteomicsmeta_proteome_analyzergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer
metagene_annotator1.0.01.0metagene_annotatorTo updateMetaGeneAnnotator gene-finding program for prokaryote and phageTo updateSequence Analysismetagene_annotatorgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
metanovo1.9.41.9.4metanovoUp-to-dateProduce targeted databases for mass spectrometry analysis.Up-to-datehttps://github.com/uct-cbio/proteomics-pipelinesProteomicsmetanovogalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo
metaquantome2.0.22.0.2metaquantomeUp-to-datequantitative analysis of microbiome taxonomy and functionUp-to-datehttps://github.com/galaxyproteomics/metaquantome/Proteomicsmetaquantomegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome
mgf_formatter1.0.01.0.0mgf-formatterUp-to-dateUp-to-datemgf_formattergalaxyp
moFF2.0.32.0.3moffUp-to-datemoFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.Up-to-datehttps://github.com/compomics/moFFProteomicsproteomics_moffgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF
morpheus2.255.0287morpheusTo updateMorpheus MS Search ApplicationTo updateProteomicsmorpheusgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus
mqppep0.1.191.64.0bioconductor-preprocesscoreTo updateMaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVATo updatehttps://github.com/galaxyproteomics/tools-galaxyp/Proteomicsmqppepgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep
msconvert3.0.20287To updatemsconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker containerTo updateProteomicsmsconvertgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
msgfplus0.52023.01.1202msgf_plusTo updateMSGF+To updateProteomicsmsgfplusgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus
msms_extractor1.0.03_0_9992proteowizardTo updateExtract MS/MS scans from the mzML file(s) based on PSM report.To updateProteomicsmsms_extractorgalaxyp
msstats4.0.04.10.0bioconductor-msstatsTo updateMSstats tool for analyzing mass spectrometry proteomic datasetsTo updatehttps://github.com/MeenaChoi/MSstatsProteomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats
msstatstmt2.0.02.10.0bioconductor-msstatstmtTo updateMSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labelingTo updatehttp://msstats.org/msstatstmt/Proteomicsmsstatstmtgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt
mt2mq1.1.0r-tidyverseTo updateTool to prepare metatranscriptomic outputs from ASaiM for MetaquantomeTo updateProteomicsmt2mqgalaxyp
mz_to_sqlite2.1.1+galaxy02.1.1mztosqliteTo updateCreates a SQLite database for proteomics dataTo updateProteomicsmz_to_sqlitegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
openms2.83.1.0openmsTo updateOpenMS Suite for LC/MS data management and analysesTo updatehttps://www.openms.de/Proteomicsopenmsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms
pathwaymatcher1.9.1pathwaymatcherTo updateReactome Pathway MatcherTo updatehttps://github.com/LuisFranciscoHS/PathwayMatcherProteomicsreactome_pathwaymatchergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher
pep_pointer0.1.3+galaxy1pythonTo updatePepPointer categorizes peptides by their genomic coordinates.To updateGenomic Interval Operations, Proteomicspep_pointergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer
pepquery1.6.22.0.2pepqueryTo updateA peptide-centric MS search engine for novel peptide identification and validation.To updatehttps://pepquery.orgProteomicspepquerygalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery
pepquery22.0.22.0.2pepqueryUp-to-datePepQuery2 peptide-centric MS search for peptide identification and validationUp-to-datehttps://pepquery.orgProteomicspepquery2galaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2
peptide_genomic_coordinate1.0.0pythonTo updateGets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite filesTo updateProteomicspeptide_genomic_coordinategalaxyp
peptideshaker4.3.6searchguiTo updatePeptideShaker and SearchGUITo updatehttp://compomics.github.ioProteomicspeptideshakergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker
pepxml_to_xlsTo updateConvert PepXML to TabularTo updateProteomicspepxml_to_xlsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls
percolator3.53.5percolatorUp-to-datePercolatorUp-to-dateProteomicspercolatorgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/percolator
pi_db_tools1.3pythonTo updateHiRIEF toolsTo updateProteomicshirieftoolsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools
pmd_fdr1.4.0r-baseTo updateCalculate Precursor Mass Discrepancy (PMD) for MS/MSTo updatehttps://github.com/slhubler/PMD-FDR-for-Galaxy-PProteomicspmd_fdrgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr
custom_pro_db1.22.01.37.1bioconductor-rgalaxyTo updateCustomProDBTo updatehttps://bioconductor.org/packages/release/bioc/html/customProDB.htmlProteomicscustom_pro_dbgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db
custom_pro_db_annotation_data_managerTo updateCustomProDB AnnotationTo updatehttps://bioconductor.org/packages/release/bioc/html/customProDB.htmlProteomicscustom_pro_db_annotation_data_managergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db
psm2sam1.3.2.1r-baseTo updatePSM to SAMTo updatehttps://bioconductor.org/packages/release/bioc/html/proBAMr.htmlProteomicspsm_to_samgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam
proteinpilot0.1To updateTo updateproteinpilotgalaxyp
retrieve_ensembl_bed0.1.0To updateRetrieve cDNA features from Ensembl REST API in BED formatTo updatehttp://rest.ensembl.org/Data Sourceretrieve_ensembl_bedgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed
translate_bed0.1.0To updateTranslate BED transcript CDS or cDNA in 3 framesTo updatehttp://rest.ensembl.org/Proteomicstranslate_bedgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed
proteomiqon_joinquantpepionswithproteins0.0.10.0.2proteomiqon-joinquantpepionswithproteinsTo updateThe tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.To updatehttps://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.htmlProteomicsproteomiqon_joinquantpepionswithproteinsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins
proteomiqon_labeledproteinquantification0.0.10.0.3proteomiqon-labeledproteinquantificationTo updateThe tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.To updatehttps://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.htmlProteomicsproteomiqon_labeledproteinquantificationgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification
proteomiqon_labelfreeproteinquantification0.0.10.0.3proteomiqon-labelfreeproteinquantificationTo updateThe tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.To updatehttps://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.htmlProteomicsproteomiqon_labelfreeproteinquantificationgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification
proteomiqon_mzmltomzlite0.0.80.0.8proteomiqon-mzmltomzliteUp-to-dateThe tool MzMLToMzLite allows to convert mzML files to mzLite files.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.htmlProteomicsproteomiqon_mzmltomzlitegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite
proteomiqon_peptidedb0.0.70.0.7proteomiqon-peptidedbUp-to-dateThe tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/PeptideDB.htmlProteomicsproteomiqon_peptidedbgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb
proteomiqon_peptidespectrummatching0.0.70.0.7proteomiqon-peptidespectrummatchingUp-to-dateGiven raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.htmlProteomicsproteomiqon_peptidespectrummatchinggalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching
proteomiqon_proteininference0.0.70.0.7proteomiqon-proteininferenceUp-to-dateMS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/ProteinInference.htmlProteomicsproteomiqon_proteininferencegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference
proteomiqon_psmbasedquantification0.0.80.0.9proteomiqon-psmbasedquantificationTo updateThe PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.To updatehttps://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.htmlProteomicsproteomiqon_psmbasedquantificationgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification
proteomiqon_psmstatistics0.0.80.0.8proteomiqon-psmstatisticsUp-to-dateThe PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/PSMStatistics.htmlProteomicsproteomiqon_psmstatisticsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics
proteore_venn_diagram2021.06.08pythonTo updateProteoRE JVenn DiagramTo updateProteomicsproteore_venn_diagramgalaxyp
protxml_to_xls0.1.0trans_proteomic_pipelineTo updateTo updateprotxml_to_xlsgalaxyp
psm_eval0.1.0binaries_for_psm_evalTo updateTo updatepsm_evalgalaxyp
psm_validation1.0.3To updateValidate PSM from Ion FragmentationTo updatehttps://github.com/galaxyproteomics/psm_fragments.gitProteomicspsm_validationgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation
pyprophet2.1.42.2.5pyprophetTo updateSemi-supervised learning and scoring of OpenSWATH results.To updatehttps://github.com/PyProphet/pyprophetProteomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet
pyteomics4.4.14.7.1pyteomicsTo updatepyteomicsPyteomicsProtein identificationProteomics, Proteomics experimentTools using the pyteomics libraryFramework for proteomics data analysis, supporting mzML, MGF, pepXML and more.To updatehttps://pyteomics.readthedocs.io/en/latest/Proteomics, Metabolomicspyteomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics
quantp1.1.21.11.6r-data.tableTo updateCorrelation between protein and transcript abundanceTo updateProteomicsquantpgalaxyp
quantwiz_iq2.02.0quantwiz-iqUp-to-dateIsobaric Quantitation using QuantWiz-IQUp-to-datehttps://sourceforge.net/projects/quantwiz/Proteomicsquantwiz_iqgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq
qupath_roi_splitter0.1.0+galaxy1geojsonTo updateSplit ROI coordinates of QuPath TMA annotation by cell typeTo updatehttps://github.com/npinter/ROIsplitterImagingqupath_roi_splittergalaxyphhttps://github.com/npinter/ROIsplitter
rawtools2.0.4rawtoolsTo updateRaw ToolsTo updatehttps://github.com/kevinkovalchik/RawToolsProteomicsrawtoolsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools
regex_find_replace1.0.3pythonTo updateUse python regular expressions to find and replace textTo updateText Manipulationregex_find_replacegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace
scaffold0.1.0scaffoldTo updateTo updatescaffoldgalaxyp
sixgill0.2.40.2.4sixgillUp-to-dateSix-frame Genome-Inferred Libraries for LC-MS/MSUp-to-dateProteomics, MetaProteomicssixgillgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill
spectrast2spectrast_irt0.1.00.11.0msproteomicstoolsTo updateFilter from spectraST files to swath input filesTo updateProteomicsspectrast2spectrast_irtgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt
spectrast2tsv0.1.00.11.0msproteomicstoolsTo updateFilter from spectraST files to swath input filesTo updateProteomicsspectrast2tsvgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv
translate_bed_sequences0.2.01.70biopythonTo updatePerform 3 frame translation of BED file augmented with a sequence columnTo updateProteomicstranslate_bed_sequencesgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences
unipept4.5.1pythonTo updateUnipept retrieves metaproteomics informationTo updatehttps://github.com/galaxyproteomics/tools-galaxypProteomicsunipeptgalaxyphttps://unipept.ugent.be/apidocs
uniprotxml_downloader2.4.0requestsTo updateDownload UniProt proteome in XML or fasta formatTo updateProteomicsuniprotxml_downloadergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
validate_fasta_database0.1.51.0validate-fasta-databaseTo updateruns Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.To updateFasta Manipulation, Proteomicsvalidate_fasta_databasegalaxyp
bio3d2.4_12.3_3r-bio3dTo updateBio3d is a program that can be used to analyse molecular dynamics trajectories.To updatehttp://thegrantlab.org/bio3d/index.phpComputational chemistrybio3dchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d
biomoldyn1.5.2scipyTo updateTools for MD analysisTo updatehttps://github.com/moldyn/Molecular Dynamics, Computational chemistrybiomoldynchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
ambertools21.10ambertoolsTo updateAmbertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.To updatehttp://ambermd.org/AmberTools.phpMolecular Dynamics, Computational chemistryambertoolschemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
packmol18.169.1packmolTo updatePACKMOL is a package for creating starting structures for Molecular Dynamics simulationsTo updatehttp://m3g.iqm.unicamp.br/packmol/home.shtmlMolecular Dynamics, Computational chemistrypackmolchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem
topologyeditors0pythonTo updateSet of python scripts and associated tool files that can be used to modify topology files.To updatehttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditorsMolecular Dynamics, Computational chemistrytopologyeditorschemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors
free_energyTo updateFree energy tools of BRIDGE.To updateMolecular Dynamics, Computational chemistryfreeenergychemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy
gromacs20222021.3gromacsTo updateGROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.To updatehttps://github.com/gromacsMolecular Dynamics, Computational chemistrygromacschemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs
mdanalysis1.0.0mdanalysisTo updateMDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulationsTo updatehttps://github.com/MDAnalysis/mdanalysisComputational chemistrymdanalysischemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
mdfileconverter1.9.7mdtrajTo updateA tool for interconverting between different MD structure and trajectory file formats.To updateMolecular Dynamics, Computational chemistrymd_converterchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter
mdslicer1.9.9mdtrajTo updateA tool for slicing trajectory files using MDTraj.To updateMolecular Dynamics, Computational chemistrymd_converterchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer
mdtraj1.9.7mdtrajTo updateMDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectoriesTo updatehttps://github.com/mdtraj/mdtrajComputational chemistrymdtrajchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
openmm1.8.1pdbfixerTo updateOpenMM is a toolkit for molecular simulation using high performance GPU code.To updatehttps://github.com/openmmMolecular Dynamics, Computational chemistryopenmmchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm
vmdTo updatevmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulationsTo updatehttps://www.ks.uiuc.edu/Research/vmd/Computational chemistryvmdchemteamhttps://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd
artbio_bam_cleaning1.10+galaxy01.19.2samtoolsTo updatefilter bam files before somatic-varscan or lumpy-smoove analysisTo updatehttp://artbio.frSAM, Variant Analysisartbio_bam_cleaningartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning
bamparse4.1.10.22.0pysamTo updateGenerates hit count lists from bam alignments.To updatehttp://artbio.frRNA, Transcriptomicsbamparseartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse
bigwig_to_bedgraph377+galaxy1448ucsc-bigwigtobedgraphTo updateConverts a bigWig file to bedGraph formatTo updatehttp://artbio.frConvert Formatsbigwig_to_bedgraphartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph
bigwig_to_wig3+galaxy0377ucsc-bigwiginfoTo updateConverts a bigWig file to Wiggle (WIG) formatTo updatehttps://artbio.frConvert Formatsbigwig_to_wigartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig
blast_to_scaffold1.1.0pythonTo updateGenerate DNA scaffold from blastn or tblastx alignments of ContigsTo updatehttp://artbio.frRNA, Sequence Analysis, Assemblyblast_to_scaffoldartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold
blast_unmatched1.0.1pythonTo updateExtract unmatched query sequences from blastTo updatehttp://artbio.frFasta Manipulationblast_unmatchedartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched
blastparser_and_hits2.7.1pythonTo updateParse blast outputs and compile hitsTo updatehttp://artbio.frAssembly, RNAblastparser_and_hitsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits
blastx_to_scaffold1.1.1pythonTo updateGenerate DNA scaffold from blastx alignment of ContigsTo updatehttp://artbio.frRNA, Sequence Analysis, Assemblyblastx_to_scaffoldartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold
cap32.0.110.2011cap3To updatecap3 wrapperTo updatehttp://artbio.frAssemblycap3artbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/cap3
cherry_pick_fasta4.1pythonTo updatePick fasta sequence with specific header contentTo updatehttp://artbio.frFasta Manipulationcherry_pick_fastaartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta
concat_multi_datasets1.4.2To updateConcatenate multiple datasets tail-to-head, including collection datasets.To updatehttp://artbio.frText Manipulationconcatenate_multiple_datasetsartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets
cpm_tpm_rpk0.5.21.3.2r-optparseTo updateGenerate CPM,TPM or RPK from raw countsTo updatehttp://artbio.frTranscriptomicscpm_tpm_rpkartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk
deseq2_normalization1.40.2+galaxy01.42.0bioconductor-deseq2To updateNormalizes gene hitlistsTo updatehttp://artbio.frRNA, Transcriptomics, Sequence Analysis, Statisticsdeseq2_normalizationartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization
embl2fa0.2To updateConverts EMBL flat format to fasta formatTo updatehttp://artbio.frText Manipulationembl2faartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa
ez_histograms3.4.42.2.1r-ggplot2To updateggplot2 histograms and density plotsTo updatehttps://github.com/tidyverse/ggplot2Visualization, Statisticsez_histogramsartbiohttps://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms
fetch_fasta_from_ncbi3.1.01.12urllib3To updateFetch fasta sequences from NCBI using eutils wrappersTo updatehttp://artbio.frFasta Manipulation, Data Sourcefetch_fasta_from_ncbiartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi
fisher_test2.32.0+galaxy02.34.0bioconductor-qvalueTo updateFisher's exact test on two-column hit lists.To updatehttp://artbio.frRNA, Statisticsfishertestartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test
gatk44.1.7.04.5.0.0gatk4To updateFind somatic variationsTo updatehttp://artbio.frVariant Analysisgatk4artbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4
get_reference_fasta0.3.2To updateObtain reference genome sequence.To updatehttp://artbio.frData Source, Fasta Manipulationget_reference_fastaartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta
gsc_center_scale4.3.1+galaxy01.3.2r-optparseTo updateCenter or scale (standardize) dataTo updatehttp://artbio.frStatisticsgsc_center_scaleartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale
gsc_filter_cells4.3.1+galaxy01.3.2r-optparseTo updateFilter single cell RNAseq data on libray depth and number of detected genesTo updatehttp://artbio.frTranscriptomicsgsc_filter_cellsartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells
gsc_filter_genes4.3.1+galaxy01.3.2r-optparseTo updateFilter genes that are detected in less than a fraction of libraries in single cell RNAseq dataTo updatehttp://artbio.frTranscriptomicsgsc_filter_genesartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes
gsc_gene_expression_correlations4.3.1+galaxy01.3.2r-optparseTo updateCompute single-cell paire-wise gene expressions correlationsTo updatehttp://artbio.frTranscriptomicsgsc_gene_expression_correlationsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations
gsc_high_dimensions_visualisation4.3+galaxy01.3.2r-optparseTo updateGenerates PCA, t-SNE and HCPC visualisationTo updatehttp://artbio.frTranscriptomics, Visualizationgsc_high_dimensions_visualisationartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization
gsc_mannwhitney_de4.1.3+galaxy01.3.2r-optparseTo updatePerform a mann-whitney differential testing between two sets of gene expression dataTo updatehttp://artbio.frTranscriptomicsgsc_mannwhitney_deartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de
gsc_scran_normalize1.28.1+galaxy01.30.0bioconductor-scranTo updateNormalize raw counts using scranTo updatehttp://artbio.frTranscriptomicsgsc_scran_normalizeartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize
gsc_signature_score2.3.9+galaxy01.3.2r-optparseTo updateCompute signature scores from single cell RNAseq dataTo updatehttp://artbio.frTranscriptomicsgsc_signature_scoreartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score
guppy0.2.2To updateA wrapper for the guppy basecaller tool from Oxford Nanopore TechnologiesTo updatehttp://artbio.frNanoporeguppy_basecallerartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/guppy
high_dim_heatmap3.1.3+galaxy02.17.0r-gplotsTo updategplot heatmap.2 function adapted for plotting large heatmapsTo updatehttps://github.com/cran/gplotsVisualizationhigh_dim_heatmapartbiohttps://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap
justdiff3.10+galaxy0diffutilsTo updateUnix diffTo updatehttp://artbio.frText Manipulationjustdiffartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff
justgzip2.8+galaxy0pigzTo updateCompress fastq sequence filesTo updatehttp://artbio.frConvert Formatsjustgzipartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip
lumpy_smoove0.2.8+galaxy10.7.1svtyperTo updateGalaxy wrapper of the lumpy-using smoove workflowTo updatehttp://artbio.frVariant Analysislumpy_smooveartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove
manta1.61.6.0mantaTo updateStructural variant and indel caller for mapped sequencing dataTo updatehttp://artbio.frVariant Analysismantaartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/manta
mapping_quality_stats0.22.01.3.2r-optparseTo updateCollects and shows the distribution of MAPQ values in a BAM alignment fileTo updatehttp://artbio.frSequence Analysis, Statisticsmapping_quality_statsartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats
mircounts1.6tarTo updateGenerates miRNA count lists from read alignments to mirBase.To updatehttp://artbio.frRNA, Transcriptomicsmircountsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts
mutational_patterns3.12.03.12.0bioconductor-mutationalpatternsUp-to-dateMutational patterns and signatures in base substitution catalogsUp-to-datehttp://artbio.frVariant Analysismutational_patternsartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns
oases1.4.00.2.09oasesTo updateShort read assemblerTo updatehttp://artbio.frAssembly, RNAoasesartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/oases
pathifier1.40.01.40.0bioconductor-pathifierUp-to-datepathifierUp-to-datehttps://Transcriptomics, Statisticspathifierartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier
pindel0.2.5b90.2.5b9pindelUp-to-datePindel detects genome-wide structural variation.Up-to-datehttp://artbio.frVariant Analysispindelartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/pindel
probecoverage0.22.00.22.0pysamUp-to-datecomputes and plots read coverage of genomic regions by sequencing datasetsUp-to-datehttp://artbio.frSequence Analysis, Genomic Interval Operations, Graphics, Statisticsprobecoverageartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage
repenrich1.5.24.0.2bioconductor-edgerTo updateRepeat element profilingTo updatehttps://github.com/nskvir/RepEnrichTranscriptomics, Variant Analysisrepenrichartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich
rsem1.3.3rsemTo updatetranscript quantification from RNA-Seq dataTo updatehttps://github.com/deweylab/RSEMTranscriptomics, RNArsemartbiohttps://github.com/artbio/tools-artbio/tree/master/tools/rsem
sambamba0.7.1+galaxy11.0sambambaTo updatefilter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAMTo updatehttp://artbio.frSAMsambambaartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba
sashimi_plot0.1.1pythonTo updateGenerates a sashimi plot from bam files.To updatehttp://artbio.frRNA, Transcriptomics, Graphics, Visualizationsashimi_plotartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot
sequence_format_converter2.2.0pythonTo updatevarious fasta to tabular conversionsTo updatehttp://artbio.frConvert Formats, Fasta Manipulationsequence_format_converterartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter
small_rna_clusters1.3.00.22.0pysamTo updateclusters small rna reads in alignment BAM filesTo updatehttp://artbio.frRNA, SAM, Graphics, Next Gen Mapperssmall_rna_clustersartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters
small_rna_maps3.1.1numpyTo updateGenerates small read maps from alignment BAM filesTo updatehttp://artbio.frRNA, SAM, Graphics, Next Gen Mapperssmall_rna_mapsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps
small_rna_signatures3.4.20.22.0pysamTo updateComputes the tendency of small RNAs to overlap with each other.To updatehttp://artbio.frRNAsmall_rna_signaturesartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures
snvtocnv3.0.0+galaxy13.0.0sequenza-utilsTo updateinfer copy number variations from a vcf file with SNVs using R sequenzaTo updatehttp://artbio.frVariant Analysissnvtocnvartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv
sr_bowtie2.3.01.3.1bowtieTo updatebowtie wrapper tool to align small RNA sequencing readsTo updatehttp://artbio.frRNA, Next Gen Mapperssr_bowtieartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie
sr_bowtie_dataset_annotation2.81.3.1bowtieTo updateMaps iteratively small RNA sequencing datasets to reference sequences.To updatehttp://artbio.frRNAsr_bowtie_dataset_annotationartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation
tarfast50.6.1pigzTo updateproduces a tar.gz archive of fast5 sequence filesTo updatehttp://artbio.frNanoporetarfast5artbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5
varscan_vaf0.1pythonTo updateCompute variant allele frequency in vcf files generated by varscan.To updatehttp://artbio.frVariant Analysisvarscan_vafartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf
xpore2.1+galaxy02.1xporeTo updateIdentification and quantification of differential RNA modifications from direct RNA sequencingTo updatehttps://github.com/GoekeLab/xporeNanoporexporeartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/xpore
yac_clipper2.5.1pythonTo updateClips 3' adapters for small RNA sequencing reads.To updatehttp://artbio.frRNA, Fastq Manipulationyac_clipperartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper
EMLassemblyline0.1.1+galaxy0r-emlassemblylineTo updateTools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versaTo updatehttps://github.com/EDIorg/EMLassemblylineEcologyemlassemblylineecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline
Ecoregionalization_workflow0.1.0+galaxy0r-baseTo updateTools to compute ecoregionalization with BRT model predictions and clustering.To updatehttps://github.com/PaulineSGN/Workflow_GalaxyEcologyecoregionalizationecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow
Geom_mean_workflow0.1.0+galaxy0r-baseTo updateTools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).To updatehttps://github.com/PaulineSGN/Galaxy_tool_moyenne_geomEcologyGeometric means (Dead wood)ecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow
PAMPA0.0.2To updateTools to compute and analyse biodiversity metricsTo updateEcologypampaecologyhttps://github.com/ColineRoyaux/PAMPA-Galaxy
ab1_fastq1.20.01.38.0bioconductor-sangerseqrTo updateTool to convert ab1 files into FASTQ filesTo updateConvert Formatsab1fastqecologyhttps://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq
champ_blocs0.0.0r-baseTo updateCompute indicators for turnover boulders fieldsTo updateEcologyecologyhttps://github.com/Marie59/champ_blocs
consensus_from_alignments1.0.0r-bioseqTo updateTool to compute a consensus sequence from several aligned fasta sequencesTo updateSequence Analysisconsalignecologyhttps://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments
data_exploration0.0.0r-tanglesTo updateExplore data through multiple statistical toolsTo updateEcologyecologyhttps://github.com/Marie59/Data_explo_tools
xarray2022.3.0xarrayTo updatexarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.To updatehttp://xarray.pydata.orgEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/
gdal3.0.0To updateGeospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.To updatehttps://www.gdal.orgEcologygdalecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal
interpolation1.0r-getoptTo updateRun IDW interpolation based on a .csv and .geojson fileTo updatehttps://github.com/AquaINFRA/galaxyEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation
medenv0.0.1pandasTo updateRetrieve environmental data from etopo, cmems and woaTo updatehttps://github.com/jeremyfix/medenvEcology, Data Sourceecologyhttps://github.com/jeremyfix/medenv
obisindicators0.0.2r-baseTo updateCompute biodiveristy indicators for marine data from obisTo updatehttps://github.com/Marie59/obisindicatorsEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
ocean0.1.15To updateAccess, process, visualise oceanographic data for the Earth SystemTo updatehttps://github.com/Marie59/FE-ft-ESG/tree/main/argoEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean
regionalgam1.5r-mgcvTo updateTo updatehttps://github.com/RetoSchmucki/regionalGAMEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam
spocc1.2.2To updateGet species occurences dataTo updatehttps://cran.r-project.org/web/packages/spocc/index.htmlEcologyspocc_occecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc
srs_tools0.0.1r-baseTo updateCompute biodiversity indicators for remote sensing data from Sentinel 2To updateEcologyecologyhttps://github.com/Marie59/Sentinel_2A/srs_tools
stoc0.0.2To updateTools to analyse STOC data.To updateEcologystocepsecologyhttps://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc
vigiechiro0.1.1To updateTools created by the vigiechiro team to analyses and identify chiro sounds files.To updatehttps://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiroEcologyvigiechiroecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro
xmlstarlet1.6.1xmlstarletTo updateTool to convert a xml file from one metadata standard to anotherTo updateConvert Formatsxmlstarletecologyhttps://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet
c3s0.2.0pythonTo updateCopernicus Climate Change Service (C3S)To updatehttps://cds.climate.copernicus.eu/cdsapp#!/search?type=datasetClimate Analysisc3sclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s
cads0.1.0pythonTo updateCopernicus Atmosphere Data Store (ADS)To updatehttps://ads.atmosphere.copernicus.eu/#!/homeClimate Analysiscadsclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads
cdo2.0.0To updateCDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.To updatehttps://code.mpimet.mpg.de/projects/cdo/Climate Analysisclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo
cesm2.1.32.1.3cesmUp-to-dateCommunity Earth System Model (CESM)Up-to-datehttps://www.cesm.ucar.edu/Climate Analysiscesmclimatehttps://github.com/ESCOMP/CESM
climate-stripes1.0.2pythonTo updateCreate climate stripes from a tabular input fileTo updatehttps://www.climate-lab-book.ac.uk/2018/warming-stripes/Climate Analysis, Visualizationclimate_stripesclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes
eodie1.0.2eodieTo updateEarth Observation Data Information ExtractorTo updatehttps://eodie.readthedocs.io/Climate Analysiseodieclimatehttps://gitlab.com/eetun-tiimi/EODIE
essential_climate_variables0.2.0pythonTo updateGet Copernicus Essential Climate Variables for assessing climate variabilityTo updatehttps://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overviewClimate Analysis, Data Sourcecds_essential_variabilityclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables
fates-emerald2.0fates-emeraldTo updateEMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host modelTo updatehttps://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_apiClimate Analysisctsm_fatesclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald
mean-per-zone0.2.0pythonTo updateCreates a png image showing statistic over areas as defined in the vector fileTo updatehttps://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/Visualization, GIS, Climate Analysismean_per_zoneclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone
psy-maps1.2.1pythonTo updateVisualization of regular geographical data on a map with psyplotTo updatehttps://github.com/Chilipp/psy-mapsVisualization, Climate Analysispsy_mapsclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps
shift-longitudes0.1.0pythonTo updateShift longitudes ranging from 0. and 360 degrees to -180. and 180. degreesTo updatehttps://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/Climate Analysisshift_longitudesclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes
smithsonian-volcanoes0.1.0pythonTo updateRetrieve data from Volcanoes of the World (VOTW) DatabaseTo updatehttps://volcano.si.edu/gvp_votw.cfmRetrieve Datasmithsonian_volcanoesclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes
droplet-barcode-plot1.6.1+galaxy20.0.1scxa-plotsTo updateMake a cell barcode plot for droplet single-cell RNA-seq QCTo updatehttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiarySequence Analysisdroplet_barcode_plotebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml
fastq_provider0.4.40.4.7atlas-fastq-providerTo updateRetrieval and download of FASTQ files from ENA and other repositories such as HCA.To updatehttps://github.com/ebi-gene-expression-group/atlas-fastq-providerData Source, RNA, Transcriptomicsatlas_fastq_providerebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider
gtf-2-gene-list1.52.0+galaxy01.1.0atlas-gene-annotation-manipulationTo updateUtility to extract annotations from Ensembl GTF files.To updatehttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiarySequence Analysisgtf2gene_listebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml
fastq_pair1.0+galaxy01.0fastq-pairTo updatePaired-end fastq pairerTo updatehttps://github.com/linsalrob/fastq-pairFastq Manipulationfastq_pairebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair
fastq_quality_trimmer0.0.14+galaxy00.0.14fastx_toolkitTo updateFASTQ trimmer based on qualityTo updatehttps://github.com/agordon/fastx_toolkitFastq Manipulationfastq_quality_trimmerebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer
fastq_utils0.25.1+galaxy00.25.2fastq_utilsTo updateSet of tools for handling fastq filesTo updatehttps://github.com/nunofonseca/fastq_utilsTranscriptomics, RNAfastq_utilsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils
salmon-kallisto-mtx-to-10x0.0.1+galaxy6scipyTo updateTransforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X dataTo updatehttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiarySequence Analysissalmon_kallisto_mtx_to_10xebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml
cell-types-analysis1.1.10.1.11cell-types-analysisTo updateTools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysisTo updateTranscriptomics, RNA, Statisticssuite_cell_types_analysisebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
data-hcav0.0.4+galaxy00.0.4hca-matrix-downloaderTo updateTools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projectsTo updateTranscriptomics, Sequence Analysissuite_human_cell_atlas_toolsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
data-scxav0.0.2+galaxy2wgetTo updateTools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/homeTo updateTranscriptomics, Sequence Analysissuite_ebi_expression_atlasebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
decoupler1.4.0+galaxy11.5.0decouplerTo updatedecoupler - Ensemble of methods to infer biological activitiesTo updatehttps://decoupler-py.readthedocs.io/en/latest/Transcriptomicssuite_decouplerebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
dropletutils1.0.40.0.5dropletutils-scriptsTo updateDe-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_dropletutilsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
garnett0.2.80.0.5garnett-cliTo updateDe-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_garnettebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
monocle30.1.40.0.9monocle3-cliTo updateDe-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_monocle3ebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
sc31.8.00.0.6sc3-scriptsTo updateDe-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_sc3ebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scanpy1.9.31.9.301scanpy-scriptsTo updatescanpy-scripts, command-line wrapper scripts around Scanpy.To updatehttps://scanpy.readthedocs.ioTranscriptomics, Sequence Analysis, RNAscanpy_scriptsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy
scater1.10.00.0.5scater-scriptsTo updateDe-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scaterebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
sccaf0.0.90.0.10sccafTo updateSCCAF: Single Cell Clustering Assessment Framework.To updatehttps://github.com/sccaf/sccafTranscriptomicsSCCAFebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf
sceasy0.0.50.0.7r-sceasyTo updateConvert scRNA data object between popular formatsTo updateTranscriptomicssceasyebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scmap1.6.30.1.0scmap-cliTo updateDe-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scmapebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scpred1.0.20.1.0scpred-cliTo updateDe-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scpredebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
seurat4.0.04.0.0seurat-scriptsUp-to-dateDe-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1Up-to-datehttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/Transcriptomics, RNA, Statistics, Sequence Analysissuite_seuratebi-gxa
ucsc-cell-browser1.0.0+galaxy11.2.5ucsc-cell-browserTo updatePython pipeline and Javascript scatter plot library for single-cell datasetsTo updatehttps://cells.ucsc.edu/Transcriptomicsucsc_cell_browserebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml
biotransformer3.0.202304033.0.20230403biotransformerUp-to-datebiotransformerBioTransformerMetabolic pathway prediction, PTM site prediction, Natural product identificationSmall molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMRBioTransformer is a tool for prediction of small molecule metabolism in mammals.BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.Up-to-datehttps://bitbucket.org/djoumbou/biotransformerjar/src/master/Metabolomicsbiotransformerrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer
filter_compounds3.1.12.3.90dev7d621d9openbabelTo updateTool for filtering organometallics/anorganic compounds from a list of compounds.To updatehttps://github.com/RECETOX/galaxytools/Metabolomicsfilter_compoundsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds
matchms0.24.00.24.2matchmsTo updatematchmsMatchmsSpectral library search, Format validation, FilteringMetabolomicsSearching, filtering and converting mass spectral libraries.Tool to import, process, clean, and compare mass spectrometry data.To updatehttps://github.com/matchms/matchmsMetabolomicsmatchmsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/matchms
misc1.0.0To updateTo updatehttps://github.com/RECETOX/galaxytoolsMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/misc
msmetaenhancer0.3.00.3.0msmetaenhancerUp-to-datemsmetaenhancerMSMetaEnhancerAnnotation, Standardisation and normalisationMetabolomics, Compound libraries and screening, Data submission, annotation and curationTool for mass spectra metadata annotation.Up-to-datehttps://github.com/RECETOX/MSMetaEnhancerMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer
msp_merge0.1.00.24.2matchmsTo updateTo updatehttps://github.com/RECETOX/galaxytoolsMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge
mzml_validator0.1.0+galaxy2lxmlTo updatemzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.To updatehttps://github.com/RECETOX/galaxytoolsMetabolomics, Proteomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator
qcxms5.2.1To updateQCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).To updatehttps://github.com/grimme-lab/QCxMSComputational chemistry, Molecular DynamicsQCxMSrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/qcxms
query0.2clickTo updateExecute an SQL statement on a set of tablesTo updateText Manipulationqueryrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/query
ramclustr1.3.01.3.1r-ramclustrTo updateramclustrRAMClustRImputation, Standardisation and normalisation, Clustering, CorrelationMetabolomicsA feature clustering algorithm for non-targeted mass spectrometric metabolomics data.To updatehttps://rdrr.io/cran/RAMClustR/Metabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr
recetox_aplcms0.12.00.12.0r-recetox-aplcmsUp-to-daterecetox-aplcmsrecetox-aplcmsChromatographic alignment, Quantification, Peak detection, Feature extraction, AlignmentMetabolomicsPeak detection tool for HRMS profile data.recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.Up-to-datehttps://github.com/RECETOX/recetox-aplcmsMetabolomicsrecetox-aplcmsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms
recetox_msfinderv3.5.2To updaterecetox-msfinderrecetox-msfinderAnnotationMetabolomicsThis is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.To updatehttps://github.com/RECETOX/recetox-msfinderMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder
recetox_xmsannotator0.10.00.10.0r-recetox-xmsannotatorUp-to-daterecetox-xmsannotatorrecetox-xMSannotatorExpression profile pathway mapping, Structure comparison, Isotopic distributions calculation, AnnotationAnnotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.Up-to-datehttps://github.com/RECETOX/recetox-xMSannotatorMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator
rem_complex1.0.0pandasTo updateRemoves molecular coordination complexes.To updatehttps://github.com/RECETOX/galaxytoolsMetabolomicsrem_complexrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex
retip0.5.4To updateretipRetipRetention time prediction, Spectrum calculation, Deisotoping, Formatting, DepositionMetabolomics, Proteomics experiment, Machine learning, Cheminformatics, ChemistryRetention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.To updatehttps://github.com/PaoloBnn/RetipMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/retip
riassigner0.4.00.4.0riassignerUp-to-dateriassignerRIAssignerStandardisation and normalisationMetabolomics, Compound libraries and screening, Data submission, annotation and curationRIAssigner is a python tool for retention index (RI) computation for GC-MS data.Up-to-datehttps://github.com/RECETOX/RIAssignerMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/riassigner
rmassbank3.0.0pythonTo updateRMassBank is an R package for processing tandem MS files and building of MassBank records.To updatehttps://github.com/MassBank/RMassBankMetabolomicsrmassbankrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank
spec2vec0.8.00.8.0spec2vecUp-to-datespec2vecSpec2VecSpectrum calculation, Spectral library search, Database search, Natural product identificationProteomics experiment, Metabolomics, Natural language processing, ProteomicsMass spectra similarity scoring using a trained Spec2Vec model.Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.Up-to-datehttps://github.com/iomega/spec2vecMetabolomicsspec2vecrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec
waveica0.2.00.2.0r-recetox-waveicaUp-to-datewaveicaWaveICAStandardisation and normalisationMetabolomicsRemoval of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.Up-to-datehttps://github.com/RECETOX/WaveICAMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/waveica
xtb6.6.1xtbTo updatePerforms semiempirical molecular optimization.To updatehttps://github.com/grimme-lab/xtbMetabolomicsxtb_molecular_optimizationrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/xtb
consolidate_vcfs1.8.21.8.2snvphyl-toolsUp-to-dateCombines freebayes and mpileup files for use by vcf2snvalignmentUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisconsolidate_vcfsnmlhttps://github.com/phac-nml/snvphyl-galaxy
filter_density1.8.21.8.2snvphyl-toolsUp-to-dateFilter out position based on distance between SNVsUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisfilter_densitynmlhttps://github.com/phac-nml/snvphyl-galaxy
filter_stats1.8.21.8.2snvphyl-toolsUp-to-dateSNVPhyl filter_statsUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisfilter_statsnmlhttps://github.com/phac-nml/snvphyl-galaxy
filter_vcf1.8.21.8.2snvphyl-toolsUp-to-dateSNVPhyl filter_vcfUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisfilter_vcfnmlhttps://github.com/phac-nml/snvphyl-galaxy
find_repeats1.8.21.8.2snvphyl-toolsUp-to-dateFind repetitive regions on a reference genome using MUMMerUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisfind_repeatsnmlhttps://github.com/phac-nml/snvphyl-galaxy
positions2snv_alignment1.8.21.8.2snvphyl-toolsUp-to-dateGenerate alignment of SNVs from SNVPhyl variant table.Up-to-datehttps://snvphyl.readthedocs.io/en/latest/Variant Analysispositions2snv_alignmentnmlhttps://github.com/phac-nml/snvphyl-galaxy
positions2snv_invariant_alignment1.8.21.8.2snvphyl-toolsUp-to-dateGenerate alignment of SNVs and non-variant positions from SNVPhyl variant table.Up-to-datehttps://snvphyl.readthedocs.io/en/latest/Variant Analysispositions2snv_invariant_alignmentnmlhttps://github.com/phac-nml/snvphyl-galaxy
snv_matrix1.8.21.8.2snvphyl-toolsUp-to-dateGenerate matrix of SNV distancesUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysissnv_matrixnmlhttps://github.com/phac-nml/snvphyl-galaxy
vcf2snvalignment1.8.21.8.2snvphyl-toolsUp-to-dateGenerates multiple alignment of variant callsUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisvcf2snvalignmentnmlhttps://github.com/phac-nml/snvphyl-galaxy
verify_map1.8.21.8.2snvphyl-toolsUp-to-dateChecks the mapping quality of all BAM(s)Up-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisverify_mapnmlhttps://github.com/phac-nml/snvphyl-galaxy
suite_snvphylTo updateSNVPhyl suite defining all dependencies for SNVPhylTo updateSequence Analysissuite_snvphyl_1_2_3nmlhttps://github.com/phac-nml/snvphyl-galaxy
cooler0.9.31.19.1htslibTo updatecooler different tools to process Hi-C from mirnylabTo updatehttps://github.com/open2c/coolerEpigeneticscoolerlldelislehttps://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml
fromHicupToJuicebox0.0.20.22.0pysamTo updateConvert the output of hicup (as sam or bam) to the input of juicebox.To updateEpigeneticsfrom_hicup_to_juiceboxlldelisle
fromgtfTobed120.11.1+galaxy10.12gffutilsTo updateConvert GTF files to BED12 formatTo updatehttps://pythonhosted.org/gffutils/contents.htmlConvert Formatsfromgtftobed12lldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12
getTn5ExtendedCoverage0.0.20.22.0pysamTo updateTake an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extensionTo updateEpigeneticsgettn5extendedcoveragelldelisle
hyperstack_to_bleach_corrected_movie2023032820231211FijiTo updateGenerate blach corrected movie from hyperstackTo updateImaginghyperstack_to_bleach_corrected_movielldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie
incucyte_stack_and_upload_omero2023122120231211FijiTo updateCombine images to stack and upload to the omero serverTo updateImagingincucyte_stack_and_upload_omerolldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero
measure_gastruloids2022121620231211fijiTo updateGet the ROI coordinates around the gastruloids as well as measurements like Area, elongation indexTo updateImagingmeasure_gastruloidslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids
omero_clean_rois_tables2023062320231211fijiTo updateRemove all ROIs and all tables on OMERO associated to an omero object and recursively up and downTo updateImagingomero_clean_rois_tableslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables
omero_get_children_ids0.1.05.11.1omero-pyTo updateGet omero id of children of an omero object idTo updateImagingomero_get_children_idslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids
omero_hyperstack_to_fluo_measurements_on_gastruloid2023080920231211fijiTo updateAnalyse Hyperstack on OMERO server to measure fluorescence levelsTo updateImagingomero_hyperstack_to_fluo_measurements_on_gastruloidlldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid
omero_hyperstack_to_gastruloid_measurements2024021420231211fijiTo updateAnalyse Hyperstack on OMERO server to segment gastruloid and compute measurementsTo updateImagingomero_hyperstack_to_gastruloid_measurementslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements
revertR2orientationInBam0.0.21.19.2samtoolsTo updateRevert the mapped orientation of R2 mates in a bam.To updateSAMrevertr2orientationinbamlldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam
upload_roi_and_measures_to_omero0.0.55.11.1omero-pyTo updateUpload the ROI coordinates and the measurements to the omero serverTo updateImagingupload_roi_and_measures_to_omerolldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero
blast2go0.0.11b2g4pipeTo updateMaps BLAST results to GO annotation termsTo updatehttps://github.com/peterjc/galaxy_blast/tree/master/tools/blast2goOntology Manipulation, Sequence Analysisblast2gopeterjchttps://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
blast_rbh0.3.01.70biopythonTo updateBLAST Reciprocal Best Hits (RBH) from two FASTA filesTo updatehttps://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbhFasta Manipulation, Sequence Analysisblast_rbhpeterjchttps://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
blastxml_to_top_descr0.1.2pythonTo updateMake table of top BLAST match descriptionsTo updatehttps://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descrConvert Formats, Sequence Analysis, Text Manipulationblastxml_to_top_descrpeterjchttps://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
make_nr0.0.21.70biopythonTo updateMake a FASTA file non-redundantTo updatehttps://github.com/peterjc/galaxy_blast/tree/master/tools/make_nrFasta Manipulation, Sequence Analysismake_nrpeterjchttps://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
ncbi_blast_plus2.14.1pythonTo updateNCBI BLAST+To updatehttps://blast.ncbi.nlm.nih.gov/Sequence Analysisncbi_blast_plusdevteamhttps://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
+ +
\ No newline at end of file diff --git a/docs/_includes/resource-table-all.html b/docs/_includes/resource-table-all.html new file mode 100644 index 00000000..45ea9754 --- /dev/null +++ b/docs/_includes/resource-table-all.html @@ -0,0 +1,34 @@ +{%- if include.tag %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + + {%- for tool in tools %} + + {% if tool.url %} + + {%- else %} + + {%- endif %} + + + + {%- endfor %} + +
ResourceDescriptionType
{{tool.name}}{{tool.name}}{{tool.description}}{{tool.type}}
+
+{%- endunless %} +
\ No newline at end of file diff --git a/docs/_includes/tools.html b/docs/_includes/tools.html new file mode 100644 index 00000000..e94c4619 --- /dev/null +++ b/docs/_includes/tools.html @@ -0,0 +1,124 @@ +{%- if include.tag %} +{%- assign tools = site.data.tools | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tools | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + + + + + + + + + + + + + + {%- for tool in tools %} + + + + + + + + + + + + + + + + + + {%- endfor %} + +
Galaxy wrapper id (+link)Galaxy wrapper versionDate of first commit of the suiteGalaxy tool idsDescriptionEDAM topic(s)EDAM operation(s)Tool usage (all time, all main servers)Sourcebio.tools (if available)Conda idConda versionbiiiStatusAvailability across Galaxies
+
+ {% if tool.["Galaxy wrapper source"] != "" %} + {{ tool.["Galaxy wrapper id"] }} + {% else %} + {{ tool.["Galaxy wrapper id"] }} + {% endif %} +
+ 		{{tool.["Galaxy wrapper version"]}}{{tool.["Date of first commit of the suite"]}} + {% if tool.["Galaxy tool ids"] %} {%- for id in tool.["Galaxy tool ids"] %} + + {{id}} + + {%- endfor %} {%- endif %} + {{tool.Description}} + {% if tool.["EDAM topic"] %} {%- for topic in tool.["EDAM topic"] %} + + {{topic}} + + {%- endfor %} {%- endif %} + + {% if tool.["EDAM operation"] %} {%- for operation in tool.["EDAM operation"] %} + + {{operation}} + + {%- endfor %} {%- endif %} + {{tool.["Tool usage (all time) - all main servers"]}} +
+ Link +
+ 		+
+ {% if tool.["bio.tool id"] != "null" %} + {{ tool.["bio.tool id"] }} + {% else %} + "" + {% endif %} +
+ 		+
+ {% if tool.["Conda id"] != "null" %} + + {{ tool.["Conda id"] }} + + {% endif %} +
+ 		+
+ {% if tool.["Conda version"] != "null" %} + + {{ tool.["Conda version"] }} + + {% endif %} +
+ 		+
+ {% if tool.biii != "null" %} + + {{ tool.biii }} + + {% endif %} +
+ 		{{tool.Status}} +
+ {% if tool.availability %} {%- for instance in tool.availability %} + + {{instance}} + + {%- endfor %} {%- endif %} +
+
+
+{%- endunless %} +
\ No newline at end of file diff --git a/docs/_includes/tutorials.html b/docs/_includes/tutorials.html new file mode 100644 index 00000000..2ad285f0 --- /dev/null +++ b/docs/_includes/tutorials.html @@ -0,0 +1,62 @@ +{%- if include.tag %} +{%- assign tools = site.data.tutorials | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tutorials | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + + + + + + {%- for tool in tools %} + + + + + + + + + + {%- endfor %} + +
Title (+link)GTN topic nameCreation dateLast updatedEDAM topic(s)EDAM operation(s)Resources available
+
+ {% if tool.title != "" %} + {{ tool.title }} + {% else %} + {{ tool.title }} + {% endif %} +
+ 		{{ tool.topic_name_human }}{{ tool.pub_date }}{{ tool.mod_date }} + {% if tool.edam_topic %} {%- for topic in tool.edam_topic %} + + {{topic}} + + {%- endfor %} {%- endif %} + + {% if tool.edam_operation %} {%- for operation in tool.edam_operation %} + + {{operation}} + + {%- endfor %} {%- endif %} + + {% if tool.slides %}Slides{%- endif %} + {% if tool.video %}Video{%- endif %} + {% if tool.hands_on %}Hands-on{%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/docs/_includes/workflows.html b/docs/_includes/workflows.html new file mode 100644 index 00000000..0c503a12 --- /dev/null +++ b/docs/_includes/workflows.html @@ -0,0 +1,76 @@ +{%- if include.tag %} +{%- assign tools = site.data.workflows | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.workflows | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + + + + + + + + {%- for tool in tools %} + + + + + + + + + + + + {%- endfor %} + +
Workflow name (+link)Creation timeLast updatedLicenseEDAM topic(s)EDAM operation(s)Tag(s)DOISource
+
+ {% if tool.name != "" %} + {{ tool.name }} + {% else %} + {{ tool.name }} + {% endif %} +
+ 		{{ tool.create_time }}{{ tool.update_time }}{{ tool.license }} + {% if tool.edam_topic %} {%- for topic in tool.edam_topic %} + + {{topic}} + + {%- endfor %} {%- endif %} + + {% if tool.edam_operation %} {%- for operation in tool.edam_operation %} + + {{operation}} + + {%- endfor %} {%- endif %} + + {% if tool.tags %} {%- for tag in tool.tags %} + + {{tag}} + + {%- endfor %} {%- endif %} + +
+ {% if tool.doi != "null" %} + DOI + {% else %} + "" + {% endif %} +
+ 		{{ tool.source }}
+
+{%- endunless %} +
\ No newline at end of file diff --git a/docs/_sass/_bootstrap_variables.scss b/docs/_sass/_bootstrap_variables.scss new file mode 100644 index 00000000..e5a9c867 --- /dev/null +++ b/docs/_sass/_bootstrap_variables.scss @@ -0,0 +1,30 @@ +// +// BioCommons Colors: https://github.com/AustralianBioCommons/umccr-dictionary/blob/main/docs/_sass/custom/custom.scss +// + +$bioc-pink:#ed087c; +$bioc-purple: #b21e8d; +$bioc-blue: #205a86; +$bioc-yellow: #f49f1d; +$bioc-teal: #5ac3b1; +$bioc-olive: #8ea869; +$bioc-green: #2cb77c; + +/*-----Theme colors-----*/ +$primary: $bioc-blue; +$secondary: $bioc-green; +$light: #f8f9fa; +$white: #FFFFFF; +$blue: $bioc-blue; +$dark: #212529; + +/*-----Custom values for Bootstrap variables-----*/ +$link-decoration: none; +$navbar-dark-color: $white; +$navbar-dark-hover-color: $white; +$navbar-light-hover-color: $light; +$navbar-light-hover-color: $dark; +$nav-link-color: $white; +$nav-link-hover-color: $light; + +// Find out which bootstrap variables you can use to fine tune the styling of your website here: https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_sass/bootstrap/_variables.scss diff --git a/docs/_sass/_custom_classes.scss b/docs/_sass/_custom_classes.scss new file mode 100644 index 00000000..41d1bb24 --- /dev/null +++ b/docs/_sass/_custom_classes.scss @@ -0,0 +1,61 @@ +// Include here all custom classes to add extra styling on top of what the theme and bootstrap variables offer. + +//Example for highlighting the active page in the navigation: +/*-----Top navigation-----*/ + +.nav-link { + color: $primary; +} + +.navbar-nav .nav-item > a { + &.active { + color: $primary; + background-color: $white; + border-radius: $border-radius; + } +} + +/* see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme*/ + +header .navbar { + background-color: $light; + .navbar-brand { + font-size: 2.25rem; + color: $primary !important; + img { + max-height: 80px; + } + } +} + +img { + @extend .img-fluid; +} + +h2 { + padding-top: 10px; + display: block; + border-top: 1px solid $table-border-color; +} + +/*-----Copied and adapted from https://github.com/elixir-europe/infectious-diseases-toolkit/blob/main/_sass/_custom_classes.scss-----*/ +/*-----Section navigation tiles-----*/ + +.navigation-tiles { + .card:hover { + box-shadow: $box-shadow; + } + + .card-header { + a:hover { + text-decoration: none; + } + h3 { + font-size: 1.2rem; + } + } + .card-text { + font-size: 0.9rem; + } +} + diff --git a/docs/_sass/_custom_variables.scss b/docs/_sass/_custom_variables.scss new file mode 100644 index 00000000..8aec0830 --- /dev/null +++ b/docs/_sass/_custom_variables.scss @@ -0,0 +1,2 @@ +// Find out which theme variables you can use to fine tune the styling of your website here: https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_sass/_variables.scss +// Copy paste theme here and change where necessary . diff --git a/docs/assets/img/biocommons_logo.png b/docs/assets/img/biocommons_logo.png new file mode 100644 index 00000000..666a1dae Binary files /dev/null and b/docs/assets/img/biocommons_logo.png differ diff --git a/docs/assets/img/galaxy_project_logo_square.png b/docs/assets/img/galaxy_project_logo_square.png new file mode 100644 index 00000000..49959f96 Binary files /dev/null and b/docs/assets/img/galaxy_project_logo_square.png differ diff --git a/docs/assets/img/microgalaxy-logo.png b/docs/assets/img/microgalaxy-logo.png new file mode 100644 index 00000000..ea12683d Binary files /dev/null and b/docs/assets/img/microgalaxy-logo.png differ diff --git a/docs/images/elixir-toolkit-theme_logo.svg b/docs/images/elixir-toolkit-theme_logo.svg new file mode 100644 index 00000000..a3e68acc --- /dev/null +++ b/docs/images/elixir-toolkit-theme_logo.svg @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..b1c4935f --- /dev/null +++ b/docs/index.md @@ -0,0 +1,11 @@ +--- +title: Tools +description: An interactive list of Galaxy tools created by the Galaxy CoDex. +datatable: true +sidebar: false +toc: false +--- + +
+{% include tools.html %} +
\ No newline at end of file diff --git a/docs/pages/about.md b/docs/pages/about.md new file mode 100644 index 00000000..61499c1a --- /dev/null +++ b/docs/pages/about.md @@ -0,0 +1,29 @@ +--- +title: About the Galaxy CoDex +description: Add a plain text description here. +--- + +Galaxy Communities Dock, aka **Galaxy Codex**, is a catalog of Galaxy resources (i.e. tools, training, workflows) that can be filtered for any community. + +The [repository located here](https://github.com/galaxyproject/galaxy_codex) stores the source for building this catalog. The catalog is automatically updated every week. + +Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and websites. + +{% include callout.html type="tip" content="Learn how to add your community in the [dedicated GTN tutorial](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html)" %} + + +## Contributors + +This resource would not be possible without the following contributors: + + + +## Acknowledgements + +The source code for the Galaxy CoDex is available here: . The additional code that [creates the interactive tables](https://github.com/galaxyproject/galaxy_codex/tree/e00632630b51e188bca11cfc35ae9eb27ace29a2/docs) has been adapted from both the [ELIXIR Toolkit Theme](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme) and [Australian BioCommons ToolFinder service](https://australianbiocommons.github.io/toolfinder/). + +This work is supported by the [Australian BioCommons](https://www.biocommons.org.au/) which is enabled by NCRIS via Bioplatforms Australia funding. + +{% include image.html file="elixir-toolkit-theme_logo.svg" alt="Elixir Toolkit Theme logo" max-width="15em" %} + + diff --git a/docs/pages/contributing.md b/docs/pages/contributing.md new file mode 100644 index 00000000..82638e31 --- /dev/null +++ b/docs/pages/contributing.md @@ -0,0 +1,15 @@ +--- +title: Contributing +--- + + +### GitHub issues + +If you think something should be added, or if you find an error, bug or mistake, please [create an issue](https://github.com/galaxyproject/galaxy_codex/issues) detailing the problem. We will do our best to fix the issue as soon as possible. You can also create an issue by clicking the `!` symbol next to the title on any of the pages. + + +### Pull Request + + + +## Thanks for contributing! diff --git a/docs/pages/project.md b/docs/pages/project.md new file mode 100644 index 00000000..6fa2d99f --- /dev/null +++ b/docs/pages/project.md @@ -0,0 +1,7 @@ +--- +title: Publications and online information for the CoDex +datatable: true +toc: false +--- + +{% include resource-table-all.html %} diff --git a/docs/pages/training.md b/docs/pages/training.md new file mode 100644 index 00000000..65ca2df6 --- /dev/null +++ b/docs/pages/training.md @@ -0,0 +1,11 @@ +--- +title: Training +description: An interactive list of Galaxy training created by the Galaxy CoDex. +datatable: true +sidebar: false +toc: false +--- + +
+{% include tutorials.html %} +
diff --git a/docs/pages/workflows.md b/docs/pages/workflows.md new file mode 100644 index 00000000..861a5b1e --- /dev/null +++ b/docs/pages/workflows.md @@ -0,0 +1,11 @@ +--- +title: Workflows +description: An interactive list of Galaxy workflows created by the Galaxy CoDex. +datatable: true +sidebar: false +toc: false +--- + +
+{% include workflows.html %} +
diff --git a/sources/bin/create_yml.py b/sources/bin/create_yml.py new file mode 100644 index 00000000..7fd5437c --- /dev/null +++ b/sources/bin/create_yml.py @@ -0,0 +1,61 @@ + +import yaml +import json +import re + +def create_tool_yml(data_source: str, yml_output_path: str): + + with open(data_source, mode="r", encoding="utf-8") as file: + data = json.load(file) + + ### https://stackoverflow.com/a/12595082 + ### https://stackoverflow.com/a/15340694 + for tool in range(len(data)): + availability = {} + for field in data[tool]: + field_value = data[tool][field] + availability_match_string = "[Aa]vailable on" + if re.search(availability_match_string, field): + instance_match_string = "[Uu]se[Gg]alaxy\.[a-z]{2}" + if re.search(instance_match_string, field): + field_name = re.search(instance_match_string, field).group(0) + if field_value != 0: + availability[field_name] = field_value + data[tool]["availability"] = availability + + with open(yml_output_path, 'w') as file: + yaml.dump(data, file, default_flow_style=False) + +create_tool_yml(data_source = "./communities/all/resources/tools.json", yml_output_path = "./docs/_data/tools.yml") + +def create_yml(data_source: str, yml_output_path: str): + + with open(data_source, mode="r", encoding="utf-8") as file: + data = json.load(file) + + with open(yml_output_path, 'w') as file: + yaml.dump(data, file, default_flow_style=False) + +create_yml(data_source = "./communities/all/resources/workflows.json", yml_output_path = "./docs/_data/workflows.yml") + + +def create_training_yml(data_source: str, yml_output_path: str, fields: list): + + with open(data_source, mode="r", encoding="utf-8") as file: + data = json.load(file) + + updated_training_data = {} + + for training in data: + id = training["id"] + updated_training_data[id] = {} + for field in fields: + if field in training: + updated_training_data[id][field] = training[field] + + with open(yml_output_path, 'w') as file: + yaml.dump(updated_training_data, file, default_flow_style=False) + +required_fields = ["title", "hands_on", "url", "slides", "mod_date", "pub_date", "version", "short_tools", "exact_supported_servers","inexact_supported_servers", "topic_name_human", "video", "edam_topic", "edam_operation", "feedback_number", "feedback_mean_note", "visitors", "pageviews", "visit_duration", "video_versions", "video_view"] + +create_training_yml(data_source = "./communities/all/resources/tutorials.json", yml_output_path = "./docs/_data/tutorials.yml", fields = required_fields)